Coulomb-explosion technique for determining geometrical structures of molecular ions

International Nuclear Information System (INIS)

Gemmell, D.S.

1981-01-01

Traditional experimental techniques (e.g. studies on photon absorption or emission) for determining the sterochemical structures of neutral molecules are extremeley difficult to apply to molecular ions because of problems in obtaining a sufficient spatial density of the ions to be studied. Recent high-resolution measurements on the energy and angle distributions of the fragments produced when fast (MeV) molecular-ion beams from an electrostatic accelerator dissociate (Coulomb explode) in thin foils and in gases, offer promising possibilities for deducing the sterochemical structures of the molecular ions constituting the incident beams. Bond lengths have been determined in this way for several diatomic projectiles (H 2+ , HeH + , CH + , NH + , OH + , N 2+ , O 2+ , etc.) with an accuracy of approx. 0.01 A. H 3+ has been demonstrated (for the first time) to be equilateral triangular and the interproton distance measured. Measurements on single fragments from CO 2+ , N 2 O + , C 3 H 3+ , and CH/sub n/ + have revealed the gross structures of the projectiles. An apparatus has recently been constructed at Argonne to permit precise measurements on fragments in coincidence. The apparatus has been tested on a known structure (OH 2+ ). The O-H bond length was found to be 1.0 +- 0.04 A and the H-O-H bond angle was measured as 110 --- 2 0 . These values are in excellent agreement with those found in optical experiments (0.999 A and 110.5 0 ). This Coulomb explosion technique can be expected to be refined in accuracy and to be extended to a wide range of molecular ions whose structures are inaccessible by other means

Controlling dynamics in diatomic systems

Indian Academy of Sciences (India)

WINTEC

Abstract. Controlling molecular energetics using laser pulses is exemplified for nuclear motion in two different diatomic systems. The problem of finding the optimized field for maximizing a desired quantum dynamical target is formulated using an iterative method. The method is applied for two diatomic sys- tems, HF and OH.

Using an electrostatic accelerator to determine the stereochemical structures of molecular ions

International Nuclear Information System (INIS)

Gemmell, D.S.

1980-01-01

Recent high-resolution measurements on the energy and angle distributions of the fragments produced when fast (MeV) molecular-ion beams from an electrostatic accelerator dissociate (Coulomb explode) in thin foils and in gases, offer promising possibilities for deducing the stereochemical structures of the molecular ions constituting the incident beams. Bond lengths have been determined in this way for several diatomic projectiles (H 2 + , HeH + , CH + , NH + , OH + , N 2 + , O 2 + , etc.) with an accuracy of approx. 0.01 A. H 3 + has been demonstrated (for the first time) to be equilateral triangular and the interproton distance measured. Measurements on single fragments from CO 2 + , N 2 O + , C 3 H 3 + , and CH/sub n/ + have revealed the gross structures of the projectiles. An apparatus has recently been constructed at Argonne to permit precise measurements on fragments in coincidence. The apparatus has been tested on a known structure (OH 2 + ). The O-H bond length was found to be 1.0 +- 0.04 A and the H-O-H bond angle was measured as 110 +- 2 0 . These values are in excellent agreement with those found in optical experiments (0.999 A and 110.5 0 ). This Coulomb explosion technique can be expected to be refined in accuracy and to be extended to a wide range of molecular ions whose structures are inaccessible by other means

Molecular Tools for the Selective Detection of Nine Diatom Species Biomarkers of Various Water Quality Levels

Directory of Open Access Journals (Sweden)

Lucia Cimarelli

2015-05-01

Full Text Available Our understanding of the composition of diatom communities and their response to environmental changes is currently limited by laborious taxonomic identification procedures. Advances in molecular technologies are expected to contribute more efficient, robust and sensitive tools for the detection of these ecologically relevant microorganisms. There is a need to explore and test phylogenetic markers as an alternative to the use of rRNA genes, whose limited sequence divergence does not allow the accurate discrimination of diatoms at the species level. In this work, nine diatom species belonging to eight genera, isolated from epylithic environmental samples collected in central Italy, were chosen to implement a panel of diatoms covering the full range of ecological status of freshwaters. The procedure described in this work relies on the PCR amplification of specific regions in two conserved diatom genes, elongation factor 1-a (eEF1-a and silicic acid transporter (SIT, as a first step to narrow down the complexity of the targets, followed by microarray hybridization experiments. Oligonucleotide probes with the potential to discriminate closely related species were designed taking into account the genetic polymorphisms found in target genes. These probes were tested, refined and validated on a small-scale prototype DNA chip. Overall, we obtained 17 highly specific probes targeting eEF1-a and SIT, along with 19 probes having lower discriminatory power recognizing at the same time two or three species. This basic array was validated in a laboratory setting and is ready for tests with crude environmental samples eventually to be scaled-up to include a larger panel of diatoms. Its possible use for the simultaneous detection of diatoms selected from the classes of water quality identified by the European Water Framework Directive is discussed.

[Research advances in heavy metals pollution ecology of diatom].

Science.gov (United States)

Ding, Teng-Da; Ni, Wan-Min; Zhang, Jian-Ying

2012-03-01

Diatom, due to its high sensitivity to environmental change, is one of the bio-indicators of aquatic ecosystem health, and some typical diatom species have been applied to indicate the heavy metals pollution of water body. With the focus on the surface water heavy metals pollution, this paper reviewed the research advances in the toxic effect of heavy metals pollution on diatom, biosorption and bioaccumulation of heavy metals by diatom, ecological adaptation mechanisms of diatom to heavy metals pollution, and roles of diatom as bio-indicator and in ecological restoration of heavy metals pollution. The growth tendency of diatom and the morphological change of frustule under heavy metals pollution as well as the differences in heavy metals biosorption and bioaccumulation by diatom, the ecological adaptation mechanisms of diatom on heavy metals surface complexation and ion exchange, and the roles of diatom as bio-indicator and in ecological restoration of heavy metals polluted water body were also discussed. This review could provide scientific evidences for the prevention of aquatic ecosystems heavy metals pollution and related early warning techniques.

Ion-atom interactions probed by photofragment spectroscopy

International Nuclear Information System (INIS)

Helm, H.

1984-01-01

Photofragment spectroscopy studies energetic and dynamical properties of molecular states interacting with dissociation continuum. So far, data for eighteen diatomic molecular ions have been gathered by this technique. This paper is a review of these investigations, introduced by a discussion of the experimental methods used. The wealth of information accessible by ion photofragment spectroscopy challenges the experimentalist in the application of innovative techniques and the theoretician for less approximate accounts of the Hamiltonian. (Auth.)

Laser-cooled atomic ions as probes of molecular ions

Energy Technology Data Exchange (ETDEWEB)

Brown, Kenneth R.; Viteri, C. Ricardo; Clark, Craig R.; Goeders, James E.; Khanyile, Ncamiso B.; Vittorini, Grahame D. [Schools of Chemistry and Biochemistry, Computational Science and Engineering and Physics, Georgia Institute of Technology, Atlanta, GA 30332 (United States)

2015-01-22

Trapped laser-cooled atomic ions are a new tool for understanding cold molecular ions. The atomic ions not only sympathetically cool the molecular ions to millikelvin temperatures, but the bright atomic ion fluorescence can also serve as a detector of both molecular reactions and molecular spectra. We are working towards the detection of single molecular ion spectra by sympathetic heating spectroscopy. Sympathetic heating spectroscopy uses the coupled motion of two trapped ions to measure the spectra of one ion by observing changes in the fluorescence of the other ion. Sympathetic heating spectroscopy is a generalization of quantum logic spectroscopy, but does not require ions in the motional ground state or coherent control of the ion internal states. We have recently demonstrated this technique using two isotopes of Ca{sup +} [Phys. Rev. A, 81, 043428 (2010)]. Limits of the method and potential applications for molecular spectroscopy are discussed.

Diatoms and the nanotechnology

International Nuclear Information System (INIS)

Toekesi, K.; Bereczky, R.J.; Lakatos, Gy.; Cserhati, C.

2004-01-01

Complete text of publication follows. During the last decade studies of interactions between highly charged ions (HCI) and solid surfaces are at the center of interest which is partly stimulated by potential future technical application such as nanofabrication. The investigation of the interactions of highly charged ions with internal surfaces recently become available due to the advances in the fabrication of micro- and nanocapillaries. These target materials offer the opportunity to observe 'hollow atom' formation in free space. Hollow atoms are an exotic form of matter where the atomic charge cloud resides in shells with large diameters while the core is virtually empty. In the past there has been an increasing amount of indirect evidence for the existence of this atomic state. Microcapillary transmission promises to provide direct evidence for the hollow atom formation for the first time. Our earlier theoretical descriptions rely on metallic microcapillaries which have proven to be quite successful in comparison with experimental data. However, since very detailed measurements have recently become available for insulator nanocapillaries, critical and precise tests of theory are only now being possible. We note, that the theoretical description of the interaction between the HCI and insulator nanocapillaries is far from being well understood. One of the key point of the experimental investigations is the preparation of the nanocapillaries. In this work we propose an alternative way to prepare insulator nanocapillaries. We take an advantage of the nature that during the evolution the cylindrical shape nanostructure was developed as a truss of diatoms. The truss of the diatoms contains roughly 99 % SiO 2 and in some cases of diatoms it form almost ideal cylindrical shape. As an example Fig. 1 shows the scanning electron micrograph of the diatom. The size of the holes in the truss are in the nanometer range (see Fig. 1a). On the basis of these properties the

Molecular evidence of the toxic effects of diatom diets on gene expression patterns in copepods.

Directory of Open Access Journals (Sweden)

Chiara Lauritano

Full Text Available Diatoms are dominant photosynthetic organisms in the world's oceans and are considered essential in the transfer of energy through marine food chains. However, these unicellular plants at times produce secondary metabolites such as polyunsaturated aldehydes and other products deriving from the oxidation of fatty acids that are collectively termed oxylipins. These cytotoxic compounds are responsible for growth inhibition and teratogenic activity, potentially sabotaging future generations of grazers by inducing poor recruitment in marine organisms such as crustacean copepods.Here we show that two days of feeding on a strong oxylipin-producing diatom (Skeletonema marinoi is sufficient to inhibit a series of genes involved in aldehyde detoxification, apoptosis, cytoskeleton structure and stress response in the copepod Calanus helgolandicus. Of the 18 transcripts analyzed by RT-qPCR at least 50% were strongly down-regulated (aldehyde dehydrogenase 9, 8 and 6, cellular apoptosis susceptibility and inhibitor of apoptosis IAP proteins, heat shock protein 40, alpha- and beta-tubulins compared to animals fed on a weak oxylipin-producing diet (Chaetoceros socialis which showed no changes in gene expression profiles.Our results provide molecular evidence of the toxic effects of strong oxylipin-producing diatoms on grazers, showing that primary defense systems that should be activated to protect copepods against toxic algae can be inhibited. On the other hand other classical detoxification genes (glutathione S-transferase, superoxide dismutase, catalase, cytochrome P450 were not affected possibly due to short exposure times. Given the importance of diatom blooms in nutrient-rich aquatic environments these results offer a plausible explanation for the inefficient use of a potentially valuable food resource, the spring diatom bloom, by some copepod species.

Cooling of molecular ion beams

International Nuclear Information System (INIS)

Wolf, A.; Krohn, S.; Kreckel, H.; Lammich, L.; Lange, M.; Strasser, D.; Grieser, M.; Schwalm, D.; Zajfman, D.

2004-01-01

An overview of the use of stored ion beams and phase space cooling (electron cooling) is given for the field of molecular physics. Emphasis is given to interactions between molecular ions and electrons studied in the electron cooler: dissociative recombination and, for internally excited molecular ions, electron-induced ro-vibrational cooling. Diagnostic methods for the transverse ion beam properties and for the internal excitation of the molecular ions are discussed, and results for phase space cooling and internal (vibrational) cooling are presented for hydrogen molecular ions

Direct determination of recoil ion detection efficiency for coincidence time-of-flight studies of molecular fragmentation

International Nuclear Information System (INIS)

Ben-Itzhak, I.; Carnes, K.D.; Ginther, S.G.; Johnson, D.T.; Norris, P.J.; Weaver, O.L.

1993-01-01

Molecular fragmentation of diatomic and small polyatomic molecules caused by fast ion impact has been studied. The evaluation of the cross sections of the different fragmentation channels depends strongly on the recoil ion detection efficiency, ε r (single ions proportional to ε r , and ion pairs to ε 2 r , etc.). A method is suggested for the direct determination of this detection efficiency. This method is based on the fact that fast H + + CH 4 collisions produce C 2+ fragments only in coincidence with H + and H + 2 fragments, that is, there is a negligible number of C 2+ singles, if any. The measured yield of C 2+ singles is therefore due to events in which the H + m of the H + m + C 2+ ion pair was not detected and thus is proportional to 1 - ε r . Methane fragmentation caused by 1 MeV proton impact is used to evaluate directly the recoil ion detection efficiency and to demonstrate the method of deriving the cross sections of all breakup channels. (orig.)

A four-component Dirac theory of ionization of a hydrogen molecular ion in a super-intense laser field

International Nuclear Information System (INIS)

Faisal, F H M

2009-01-01

In this communication, a four-component Dirac theory of ionization of a hydrogen molecular ion, H + 2 , in a super-intense laser field is presented. Analytic expressions for the spin-specific as well as the total ionization currents emitted from the ground state of the ion are derived. The results are given for arbitrary intensity, frequency, wavenumber and polarization of the field, and for the up or down spin of the bound and ionized states of the electron. They also apply for the case of inner-shell ionization of analogous heavier diatomic molecular ions. The presence of molecular two-slit interference effect, first found in the non-relativistic case, the spin-flip ionization current, and an asymmetry of the up- and down-spin currents similar to that predicted in the atomic case, is found to hold for the present relativistic molecular ionic case as well. The possibility of controlling the spin of the dominant ionization current in any direction by simply selecting the handedness of a circularly polarized incident laser field is pointed out. Finally, we note that the present results obtained within the strong field 'KFR' ansatz open up the way for an analogous fully relativistic four-component treatment for ionization of polyatomic molecules and clusters in super-intense laser fields. (fast track communication)

Molecular ion photofragment spectroscopy

International Nuclear Information System (INIS)

Bustamente, S.W.

1983-11-01

A new molecular ion photofragment spectrometer is described which features a supersonic molecular beam ion source and a radio frequency octapole ion trap interaction region. This unique combination allows several techniques to be applied to the problem of detecting a photon absorption event of a molecular ion. In particular, it may be possible to obtain low resolution survey spectra of exotic molecular ions by using a direct vibrational predissociation process, or by using other more indirect detection methods. The use of the spectrometer is demonstrated by measuring the lifetime of the O 2 + ( 4 π/sub u/) metastable state which is found to consist of two main components: the 4 π/sub 5/2/ and 4 π/sub -1/2/ spin components having a long lifetime (approx. 129 ms) and the 4 π/sub 3/2/ and 4 π/sub 1/2/ spin components having a short lifetime (approx. 6 ms)

Low-Molecular-Weight Metabolites from Diatoms: Structures, Biological Roles and Biosynthesis

Directory of Open Access Journals (Sweden)

Valentin Stonik

2015-06-01

Full Text Available Diatoms are abundant and important biological components of the marine environment that biosynthesize diverse natural products. These microalgae are rich in various lipids, carotenoids, sterols and isoprenoids, some of them containing toxins and other metabolites. Several groups of diatom natural products have attracted great interest due to their potential practical application as energy sources (biofuel, valuable food constituents, and prospective materials for nanotechnology. In addition, hydrocarbons, which are used in climate reconstruction, polyamines which participate in biomineralization, new apoptotic agents against tumor cells, attractants and deterrents that regulate the biochemical communications between marine species in seawaters have also been isolated from diatoms. However, chemical studies on these microalgae are complicated by difficulties, connected with obtaining their biomass, and the influence of nutrients and contaminators in their environment as well as by seasonal and climatic factors on the biosynthesis of the corresponding natural products. Overall, the number of chemically studied diatoms is lower than that of other algae, but further studies, particularly those connected with improvements in the isolation and structure elucidation technique as well as the genomics of diatoms, promise both to increase the number of studied species with isolated biologically active natural products and to provide a clearer perception of their biosynthesis.

Radiational and energetic characteristics of diatomic molecules (data base)

International Nuclear Information System (INIS)

Kuznetsova, L.A.; Pazyuk, E.A.; Stolyarov, A.V.

1993-01-01

Data base on radiational and energetic characteristics of diatomic molecules was created. The base consists of two parts: reference system and recommended data system. The reference system contains the information about studies of radiational and energetic parameters of more than 1500 electronic states and 1700 electron transfers for ∼ 350 diatomic molecules and their ions. The base bibliography includes ∼ 3000 publications. 11 refs., 1 figs

Dissociation and ionization of molecular ions by ultra-short intense laser pulses probed by coincidence 3D momentum imaging

International Nuclear Information System (INIS)

Ben-Itzhak, Itzik; Wang, Pengqian; Xia, Jiangfan; Max Sayler, A.; Smith, Mark A.; Maseberg, J.W.; Carnes, Kevin D.; Esry, Brett D.

2005-01-01

We have experimentally explored laser-induced dissociation and ionization of diatomic molecular ions using coincidence 3D momentum imaging. The vibrationally excited molecular ion beam (4-8 keV) is crossed by an ultrafast intense laser beam (28-200 fs, 10 13 -10 14 W/cm 2 ). The resulting fragments are recorded in coincidence by a time and position-sensitive detector. Complete angular distributions and kinetic energy release maps are reconstructed from the measured dissociation-momentum vectors. The angular distribution of the H + + H fragments was found to be strongly correlated to their kinetic energy release upon dissociation. Low KER was associated with very narrow angular distributions and high KER with distributions peaking away from the laser polarization. Ionization was found to be smaller than dissociation and increased with laser intensity. The H + + H + fragments have a very narrow angular distribution along the laser polarization

Dynamics in ion-molecule collisions at high velocities: One- and two-electron processes

International Nuclear Information System (INIS)

Wang, Yudong.

1992-01-01

This dissertation addresses the dynamic interactions in ion-molecule collisions. Theoretical methods are developed for single and multiple electron transitions in fast collisions with diatomic molecules by heavy-ion projectiles. Various theories and models are developed to treat the three basic inelastic processes (excitation, ionization and charge transfer) involving one and more electrons. The development, incorporating the understanding of ion-atom collision theories with some unique characteristics for molecular targets, provides new insights into phenomena that are absent from collisions with atomic targets. The influence from the multiple scattering centers on collision dynamics is assessed. For diatomic molecules, effects due to a fixed molecular orientation or alignment are calculated and compared with available experimental observations. Compared with excitation and ionization, electron capture, which probes deeper into the target, presents significant two-center interference and strong orientation dependence. Attention has been given in this dissertation to exploring mechanisms for two-and multiple electron transitions. Application of independent electron approximation to transfer excitation from molecular hydrogen is studied. Electron-electron interaction originated from projectile and target nuclear centers is studied in conjunction with the molecular nature of target. Limitations of the present theories and models as well as possible new areas for future theoretical and experimental applications are also discussed. This is the first attempt to describe multi-electron processes in molecular dynamics involving fast highly charged ions

Determining the stereochemical structures of molecular ions by ''Coulomb-explosion'' techniques with fast (MeV) molecular ion beams

International Nuclear Information System (INIS)

Gemmell, D.S.

1980-01-01

Recent studies on the dissociation of fast (MeV) molecular ion beams in thin foils suggest a novel alternative approach to the determination of molecular ion structures. In this article we review some recent high-resolution studies on the interactions of fast molecular ion beams with solid and gaseous targets and indicate how such studies may be applied to the problem of determining molecular ion structures. The main features of the Coulomb explosion of fast-moving molecular ion projectiles and the manner in which Coulomb-explosion techniques may be applied to the problem (difficult to attack by more conventional means) of determining the stereochemical structures of molecular ions has been described in this paper. Examples have been given of early experiments designed to elicit structure information. The techniques are still in their infancy, and it is to be expected that as both the technology and the analysis are refined, the method will make valuable contributions to the determination of molecular ion structures

Superatom spectroscopy and the electronic state correlation between elements and isoelectronic molecular counterparts.

Science.gov (United States)

Peppernick, Samuel J; Gunaratne, K D Dasitha; Castleman, A W

2010-01-19

Detailed in the present investigation are results pertaining to the photoelectron spectroscopy of negatively charged atomic ions and their isoelectronic molecular counterparts. Experiments utilizing the photoelectron imaging technique are performed on the negative ions of the group 10 noble metal block (i.e. Ni-, Pd-, and Pt-) of the periodic table at a photon energy of 2.33 eV (532 nm). The accessible electronic transitions, term energies, and orbital angular momentum components of the bound electronic states in the atom are then compared with photoelectron images collected for isoelectronic early transition metal heterogeneous diatomic molecules, M-X- (M = Ti,Zr,W; X = O or C). A superposition principle connecting the spectroscopy between the atomic and molecular species is observed, wherein the electronic structure of the diatomic is observed to mimic that present in the isoelectronic atom. The molecular ions studied in this work, TiO-, ZrO-, and WC- can then be interpreted as possessing superatomic electronic structures reminiscent of the isoelectronic elements appearing on the periodic table, thereby quantifying the superatom concept.

Electron-impact excitation of molecular ions

International Nuclear Information System (INIS)

Neufeld, D.A.; Dalgarno, A.

1989-01-01

A simple expression is derived that relates the rate coefficient for dipole-allowed electron-impact excitation of a molecular ion in the Coulomb-Born approximation to the Einstein A coefficient for the corresponding radiative decay. Results are given for several molecular ions of astrophysical interest. A general analytic expression is obtained for the equilibrium rotational level populations in the ground vibrational state of any molecular ion excited by collisions with electrons. The expression depends only upon the electron temperature, the electron density, and the rotational constant of the molecular ion. A similar expression is obtained for neutral polar molecules

Seasonal variations in fouling diatom communities on the Yantai coast

Science.gov (United States)

Yang, Cuiyun; Wang, Jianhua; Yu, Yang; Liu, Sujing; Xia, Chuanhai

2015-03-01

Fouling diatoms are a main component of biofilm, and play an important role in marine biofouling formation. We investigated seasonal variations in fouling diatom communities that developed on glass slides immersed in seawater, on the Yantai coast, northern Yellow Sea, China, using microscopy and molecular techniques. Studies were conducted during 2012 and 2013 over 3, 7, 14, and 21 days in each season. The abundance of attached diatoms and extracellular polymeric substances increased with exposure time of the slides to seawater. The lowest diatom density appeared in winter and the highest species richness and diversity were found in summer and autumn. Seasonal variation was observed in the structure of fouling diatom communities. Pennate diatoms Cylindrotheca, Nitzschia, Navicula, Amphora, Gomphonema, and Licmophora were the main fouling groups. Cylindrotheca sp. dominated in the spring. Under laboratory culture conditions, we found that Cylindrotheca grew very fast, which might account for the highest density of this diatom in spring. The lower densities in summer and autumn might result from the emergence of fouling animals and environmental factors. The Cylindrotheca sp. was identified as Cylindrotheca closterium using18S rDNA sequencing. The colonization process of fouling diatoms and significant seasonal variation in this study depended on environmental and biological factors. Understanding the basis of fouling diatoms is essential and important for developing new antifouling techniques.

Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms

Science.gov (United States)

McQuaid, Jeffrey B.; Kustka, Adam B.; Oborník, Miroslav; Horák, Aleš; McCrow, John P.; Karas, Bogumil J.; Zheng, Hong; Kindeberg, Theodor; Andersson, Andreas J.; Barbeau, Katherine A.; Allen, Andrew E.

2018-03-01

In vast areas of the ocean, the scarcity of iron controls the growth and productivity of phytoplankton. Although most dissolved iron in the marine environment is complexed with organic molecules, picomolar amounts of labile inorganic iron species (labile iron) are maintained within the euphotic zone and serve as an important source of iron for eukaryotic phytoplankton and particularly for diatoms. Genome-enabled studies of labile iron utilization by diatoms have previously revealed novel iron-responsive transcripts, including the ferric iron-concentrating protein ISIP2A, but the mechanism behind the acquisition of picomolar labile iron remains unknown. Here we show that ISIP2A is a phytotransferrin that independently and convergently evolved carbonate ion-coordinated ferric iron binding. Deletion of ISIP2A disrupts high-affinity iron uptake in the diatom Phaeodactylum tricornutum, and uptake is restored by complementation with human transferrin. ISIP2A is internalized by endocytosis, and manipulation of the seawater carbonic acid system reveals a second-order dependence on the concentrations of labile iron and carbonate ions. In P. tricornutum, the synergistic interaction of labile iron and carbonate ions occurs at environmentally relevant concentrations, revealing that carbonate availability co-limits iron uptake. Phytotransferrin sequences have a broad taxonomic distribution and are abundant in marine environmental genomic datasets, suggesting that acidification-driven declines in the concentration of seawater carbonate ions will have a negative effect on this globally important eukaryotic iron acquisition mechanism.

First Morphological and Molecular Evidence of the Negative Impact of Diatom-Derived Hydroxyacids on the Sea Urchin Paracentrotus lividus

Science.gov (United States)

Varrella, Stefano; Romano, Giovanna; Ruocco, Nadia; Ianora, Adrianna; Bentley, Matt G.; Costantini, Maria

2016-01-01

Oxylipins (including polyunsaturated aldehydes [PUAs], hydoxyacids, and epoxyalcohols) are the end-products of a lipoxygenase/hydroperoxide lyase metabolic pathway in diatoms. To date, very little information is available on oxylipins other than PUAs, even though they represent the most common oxylipins produced by diatoms. Here, we report, for the first time, on the effects of 2 hydroxyacids, 5- and 15-HEPE, which have never been tested before, using the sea urchin Paracentrotus lividus as a model organism. We show that HEPEs do induce developmental malformations but at concentrations higher when compared with PUAs. Interestingly, HEPEs also induced a marked developmental delay in sea urchin embryos, which has not hitherto been reported for PUAs. Recovery experiments revealed that embryos do not recover following treatment with HEPEs. Finally, we report the expression levels of 35 genes (involved in stress, development, differentiation, skeletogenesis, and detoxification processes) to identify the molecular targets affected by HEPEs. We show that the 2 HEPEs have very few common molecular targets, specifically affecting different classes of genes and at different times of development. In particular, 15-HEPE switched on fewer genes than 5-HEPE, upregulating mainly stress-related genes at a later pluteus stage of development. 5-HEPE was stronger than 15-HEPE, targeting 24 genes, mainly at the earliest stages of embryo development (at the blastula and swimming blastula stages). These findings highlight the differences between HEPEs and PUAs and also have important ecological implications because many diatom species do not produce PUAs, but rather these other chemicals are derived from the oxidation of fatty acids. PMID:26984781

Are Diatoms “Green” Aluminosilicate Synthesis Microreactors for Future Catalyst Production?

Directory of Open Access Journals (Sweden)

Lydia Köhler

2017-12-01

Full Text Available Diatom biosilica may offer an interesting perspective in the search for sustainable solutions meeting the high demand for heterogeneous catalysts. Diatomaceous earth (diatomite, i.e., fossilized diatoms, is already used as adsorbent and carrier material. While diatomite is abundant and inexpensive, freshly harvested and cleaned diatom cell walls have other advantages, with respect to purity and uniformity. The present paper demonstrates an approach to modify diatoms both in vivo and in vitro to produce a porous aluminosilicate that is serving as a potential source for sustainable catalyst production. The obtained material was characterized at various processing stages with respect to morphology, elemental composition, surface area, and acidity. The cell walls appeared normal without morphological changes, while their aluminum content was raised from the molar ratio n(Al:n(Si 1:600 up to 1:50. A specific surface area of 55 m2/g was measured. The acidity of the material increased from 149 to 320 µmol NH3/g by ion exchange, as determined by NH3 TPD. Finally, the biosilica was examined by an acid catalyzed test reaction, the alkylation of benzene. While the cleaned cell walls did not catalyze the reaction at all, and the ion exchanged material was catalytically active. This demonstrates that modified biosilica does indeed has potential as a basis for future catalytically active materials.

Biophotonics of diatoms

DEFF Research Database (Denmark)

Gössling, Johannes Wilhelm

Diatoms are unicellular microalgae present in all aquatic environments on earth. Due to their high photosynthetic productivity and abundance, diatoms are main components of aquatic food webs and among the main contributors of global photosynthetic carbon fixation. A unique feature of diatoms...

Radiation damage in diatomic materials at high doses

International Nuclear Information System (INIS)

Hobbs, L.W.; Hughes, A.E.

1975-10-01

Radiation effects in diatomic materials can differ structurally from those in metals because of the need to take into account different displacement rates on the two sublattices and the inevitable stoichiometric implications; in most diatomic insulators the anion species has the greater displacement cross section. Anion point defect stabilisation in heavily-irradiated (0.1 to 10 dpa) diatomic insulators has been studied using radiolysis of alkali and alkaline earth halides. A temperatures > 0.3 Tsub(m), all anion defects are mobile and can aggregate. Aggregation of anion interstitials results in creation of perfect dislocation loops without the need for primary cation displacements; simultaneous formation of substitutional anion molecular centres provides the necessary cation interstitials. Aggregation of anion vacancies leads to formation of metallic inclusions of the cation species, in some cases in an ordered array, which is the analogue, on a single sublattice, to the void lattice in metals. Availability of sinks for both anion interstitials and anion vacancies yields defect growth kinetics similar to those observed during formation of voids in irradiated metals, and a very high level of damage (approximately 10%) can be sustained in the lattice. The width of the temperature region concerned is much narrower, however, due to the possibility of recombination of aggregated or re-emitted anion vacancies with mobile or dispersed anion molecular defects; the latter can also aggregate to form fluid anion molecular inclusions and so complete the decomposition of the solid into separate phases of its constituent elements. (author)

Laser induced fluorescence of trapped molecular ions

Energy Technology Data Exchange (ETDEWEB)

Grieman, F.J.

1979-10-01

An experimental apparatus for obtaining the optical spectra of molecular ions is described. The experimental technique includes the use of three dimensional ion trapping, laser induced fluorescence, and gated photon counting methods. The ions, which are produced by electron impact, are confined in a radio-frequency quadrupole ion trap of cylindrical design. Because the quadrupole ion trap allows mass selection of the molecular ion desired for study, the analysis of the spectra obtained is greatly simplified. The ion trap also confines the ions to a region easily probed by a laser beam. 18 references.

Laser induced fluorescence of trapped molecular ions

International Nuclear Information System (INIS)

Grieman, F.J.

1979-10-01

An experimental apparatus for obtaining the optical spectra of molecular ions is described. The experimental technique includes the use of three dimensional ion trapping, laser induced fluorescence, and gated photon counting methods. The ions, which are produced by electron impact, are confined in a radio-frequency quadrupole ion trap of cylindrical design. Because the quadrupole ion trap allows mass selection of the molecular ion desired for study, the analysis of the spectra obtained is greatly simplified. The ion trap also confines the ions to a region easily probed by a laser beam. 18 references

Production and sympathetic cooling of complex molecular ions

Energy Technology Data Exchange (ETDEWEB)

Zhang, Chaobo

2008-06-24

This thesis reports on experimental and theoretical studies of the sympathetic cooling of complex molecular ions demonstrating that this general method for cooling atomic and molecular ions is reliable and efficient. For this purpose, complex molecular ions and barium ions have been confined simultaneously in a linear Paul trap. The complex molecular ions are generated in an electrospray ionization system and transferred to the trap via a 2 m long octopole ion guide. These molecular ions are pre-cooled by room temperature helium buffer gas so that they can be captured by the trap. The atomic barium ions are loaded from a barium evaporator oven and are laser-cooled by a 493 nm cooling laser and a 650 nm repumping laser. Due to the mutual Coulomb interaction among these charged particles, the kinetic energy of the complex molecular ions can be reduced significantly. In our experiments we have demonstrated the sympathetic cooling of various molecules (CO{sub 2}, Alexa Fluor 350, glycyrrhetinic acid, cytochrome c) covering a wide mass range from a few tens to 13000 amu. In every case the molecular ions could be cooled down to millikelvin temperatures. Photo-chemical reactions of the {sup 138}Ba{sup +} ions in the ({sup 2}P{sub 1/2}) excited state with gases such as O{sub 2}, CO{sub 2}, or N{sub 2}O, could be observed. If the initial {sup 138}Ba{sup +} ion ensemble is cold, the produced {sup 138}BaO{sup +} ions are cold as well, with a similar temperature as the laser-cooled barium ions (a few tens of millikelvin). The back-reaction of {sup 138}BaO{sup +} ions with neutral CO to {sup 138}Ba{sup +} is possible and was observed in our experiments as well. A powerful molecular dynamics (MD) simulation program has been developed. With this program dynamic properties of ion ensembles, such as sympathetic interactions or heating effects, have been investigated and experimental results have been analyzed to obtain, for example, ion numbers and temperatures. Additionally, the

Production and sympathetic cooling of complex molecular ions

International Nuclear Information System (INIS)

Zhang, Chaobo

2008-01-01

This thesis reports on experimental and theoretical studies of the sympathetic cooling of complex molecular ions demonstrating that this general method for cooling atomic and molecular ions is reliable and efficient. For this purpose, complex molecular ions and barium ions have been confined simultaneously in a linear Paul trap. The complex molecular ions are generated in an electrospray ionization system and transferred to the trap via a 2 m long octopole ion guide. These molecular ions are pre-cooled by room temperature helium buffer gas so that they can be captured by the trap. The atomic barium ions are loaded from a barium evaporator oven and are laser-cooled by a 493 nm cooling laser and a 650 nm repumping laser. Due to the mutual Coulomb interaction among these charged particles, the kinetic energy of the complex molecular ions can be reduced significantly. In our experiments we have demonstrated the sympathetic cooling of various molecules (CO 2 , Alexa Fluor 350, glycyrrhetinic acid, cytochrome c) covering a wide mass range from a few tens to 13000 amu. In every case the molecular ions could be cooled down to millikelvin temperatures. Photo-chemical reactions of the 138 Ba + ions in the ( 2 P 1/2 ) excited state with gases such as O 2 , CO 2 , or N 2 O, could be observed. If the initial 138 Ba + ion ensemble is cold, the produced 138 BaO + ions are cold as well, with a similar temperature as the laser-cooled barium ions (a few tens of millikelvin). The back-reaction of 138 BaO + ions with neutral CO to 138 Ba + is possible and was observed in our experiments as well. A powerful molecular dynamics (MD) simulation program has been developed. With this program dynamic properties of ion ensembles, such as sympathetic interactions or heating effects, have been investigated and experimental results have been analyzed to obtain, for example, ion numbers and temperatures. Additionally, the feasibility of nondestructive spectroscopy via an optical dipole excitation

Shifting of infrared radiation using rotational raman resonances in diatomic molecular gases

Science.gov (United States)

Kurnit, Norman A.

1980-01-01

A device for shifting the frequency of infrared radiation from a CO.sub.2 laser by stimulated Raman scattering in either H.sub.2 or D.sub.2. The device of the preferred embodiment comprises an H.sub.2 Raman laser having dichroic mirrors which are reflective for 16 .mu.m radiation and transmittive for 10 .mu.m, disposed at opposite ends of an interaction cell. The interaction cell contains a diatomic molecular gas, e.g., H.sub.2, D.sub.2, T.sub.2, HD, HT, DT and a capillary waveguide disposed within the cell. A liquid nitrogen jacket is provided around the capillary waveguide for the purpose of cooling. In another embodiment the input CO.sub.2 radiation is circularly polarized using a Fresnel rhomb .lambda./4 plate and applied to an interaction cell of much longer length for single pass operation.

The effects of phosphorus limitation on carbon metabolism in diatoms.

Science.gov (United States)

Brembu, Tore; Mühlroth, Alice; Alipanah, Leila; Bones, Atle M

2017-09-05

Phosphorus is an essential element for life, serving as an integral component of nucleic acids, lipids and a diverse range of other metabolites. Concentrations of bioavailable phosphorus are low in many aquatic environments. Microalgae, including diatoms, apply physiological and molecular strategies such as phosphorus scavenging or recycling as well as adjusting cell growth in order to adapt to limiting phosphorus concentrations. Such strategies also involve adjustments of the carbon metabolism. Here, we review the effect of phosphorus limitation on carbon metabolism in diatoms. Two transcriptome studies are analysed in detail, supplemented by other transcriptome, proteome and metabolite data, to gain an overview of different pathways and their responses. Phosphorus, nitrogen and silicon limitation responses are compared, and similarities and differences discussed. We use the current knowledge to propose a suggestive model for the carbon flow in phosphorus-replete and phosphorus-limited diatom cells.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Authors.

Understanding Molecular Ion-Neutral Atom Collisions for the Production of Ultracold Molecular Ions

Science.gov (United States)

2016-06-06

2012): 0. doi: 10.1103/PhysRevLett.109.223002 Kuang Chen, Scott T. Sullivan, Wade G. Rellergert, Eric R. Hudson. Measurement of the Coulomb Logarithm...or fellowships for further studies in science, mathematics, engineering or technology fields: Student Metrics This section only applies to graduating...clouds of Ba+ ions and Ca atoms. Due to the strong Coulomb interaction, the Ba+ ions quickly cool the molecular ion translation motion, while the

Behavior of the Position-Spread Tensor in Diatomic Systems.

Science.gov (United States)

Brea, Oriana; El Khatib, Muammar; Angeli, Celestino; Bendazzoli, Gian Luigi; Evangelisti, Stefano; Leininger, Thierry

2013-12-10

The behavior of the Position-Spread Tensor (Λ) in a series of light diatomic molecules (either neutral or negative ions) is investigated at a Full Configuration Interaction level. This tensor, which is the second moment cumulant of the total position operator, is invariant with respect to molecular translations, while its trace is also rotationally invariant. Moreover, the tensor is additive in the case of noninteracting subsystems and can be seen as an intrinsic property of a molecule. In the present work, it is shown that the longitudinal component of the tensor, Λ∥, which is small for internuclear distances close to the equilibrium, tends to grow if the bond is stretched. A maximum is reached in the region of the bond breaking, then Λ∥ decreases and converges toward the isolated-atom value. The degenerate transversal components, Λ⊥, on the other hand, usually have a monotonic growth toward the atomic value. The Position Spread is extremely sensitive to reorganization of the molecular wave function, and it becomes larger in the case of an increase of the electron mobility, as illustrated by the neutral-ionic avoided crossing in LiF. For these reasons, the Position Spread can be an extremely useful property that characterizes the nature of the wave function in a molecular system.

Studies on new antifreeze protein from the psychrophilic diatom ...

African Journals Online (AJOL)

Studies on new antifreeze protein from the psychrophilic diatom, Fragilariopsis cylindrus. ... African Journal of Biotechnology. Journal Home · ABOUT THIS ... The predicted gene product, AfpA, had a molecular mass of 27 kDa. Expression of ...

Recharging of a screened ion on the molecular ion

International Nuclear Information System (INIS)

Karbovanets, M.I.; Lazur, V.Yu.; Yudin, G.L.; Gosudarstvennyj Komitet po Ispol'zovaniyu Atomnoj Ehnergii SSSR, Obninsk. Fiziko-Ehnergeticheskij Inst.)

1987-01-01

Charge exchange of a screened ion on a molecular ion is studied in the Oppenheimer-Brinkman-Cramers approximation. To calculate ion exchange probabilities and cross sections summed over the final degenerated electron states method of Green functions analogous to that applied earlier in the direct Coulomb excitation theory and atomic ionization is developed

Molecular basis of chromatic adaptation in pennate diatom Phaeodactylum tricornutum

Czech Academy of Sciences Publication Activity Database

Herbstová, Miroslava; Bína, David; Koník, P.; Gardian, Zdenko; Vácha, František; Litvín, Radek

2015-01-01

Roč. 1847, 6-7 (2015), s. 534-543 ISSN 0005-2728 R&D Projects: GA ČR GBP501/12/G055 Institutional support: RVO:60077344 Keywords : Chromatic adaptation * Diatom * Heterokonta * Light harvesting antenna Subject RIV: CE - Biochemistry Impact factor: 4.864, year: 2015

Molecular ions, Rydberg spectroscopy and dynamics

International Nuclear Information System (INIS)

Jungen, Ch.

2015-01-01

Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering

Molecular ions, Rydberg spectroscopy and dynamics

Energy Technology Data Exchange (ETDEWEB)

Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)

2015-01-22

Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.

Molecular and negative ion production by a standard electron cyclotron resonance ion source

Energy Technology Data Exchange (ETDEWEB)

Racz, R. [Institute of Nuclear Research (ATOMKI), Bem ter 18/c, H-4026 Debrecen (Hungary); University of Debrecen, Egyetem ter 1, H-4010 Debrecen (Hungary); Biri, S.; Juhasz, Z.; Sulik, B. [Institute of Nuclear Research (ATOMKI), Bem ter 18/c, H-4026 Debrecen (Hungary); Palinkas, J. [University of Debrecen, Egyetem ter 1, H-4010 Debrecen (Hungary)

2012-02-15

Molecular and negative ion beams, usually produced in special ion sources, play an increasingly important role in fundamental and applied atomic physics. The ATOMKI-ECRIS is a standard ECR ion source, designed to provide highly charged ion (HCI) plasmas and beams. In the present work, H{sup -}, O{sup -}, OH{sup -}, O{sub 2}{sup -}, C{sup -}, C{sub 60}{sup -} negative ions and H{sub 2}{sup +}, H{sub 3}{sup +}, OH{sup +}, H{sub 2}O{sup +}, H{sub 3}O{sup +}, O{sub 2}{sup +} positive molecular ions were generated in this HCI-ECRIS. Without any major modification in the source and without any commonly applied tricks (such as usage of cesium or magnetic filter), negative ion beams of several {mu}A and positive molecular ion beams in the mA range were successfully obtained.

Channeling of molecular ions with relativistic energy

International Nuclear Information System (INIS)

Azuma, Toshiyuki; Muranaka, Tomoko; Kondo, Chikara; Hatakeyama, Atsushi; Komaki, Kenichiro; Yamazaki, Yasunori; Takabayashi, Yuichi; Murakami, Takeshi; Takada, Eiichi

2003-01-01

When energetic ions are injected into a single crystal parallel to a crystal axis or plane, they proceed in an open space guided by the crystal potential without colliding with atoms in the atomic plane or string, which is called channeling. We aimed to study dynamics of molecular ions, H 2 + , of 160 MeV/u and their fragment ions, H + ions in a Si crystal under the channeling condition. The molecular ions, H 2 + , are soon ionized, i.e. electron-stripped in the crystal, and a pair of bare nuclei, H + ions, travels in the crystal potential with mutual Coulomb repulsion. We developed a 2D position sensitive detector for the angular-distribution measurement of the H + ions transmitted through the crystal, and observed the detailed angular distribution. In addition we measured the case of H + on incidence for comparison. As a result, the channeled component and non-channeling were clearly separated. The incident angular divergence is critical to discuss the effect of Coulomb explosion of molecular H 2 + ions. (author)

Symmetries and rotational line intensities in diatomic molecules

International Nuclear Information System (INIS)

Veseth, L.

1986-02-01

The general theory of angular momenta and the full rotation group is used to reconsider the theory of the intensity factors of rotational lines in the spectra of diatomic molecules (Hoenl-London factors). It is shown that the use of the rotational symmetry (rotation matrices) leads to compact derivations of the symmetry properties of the molecular wave functions, as well as the matrix elements of the transitions operator. The present work is restricted to spin-allowed electric dipole transitions, and the general sum rule characteristic of this type of transitions is rederived by use of the general angular momentum theory. A main purpose of the present work has been to provide a unified theoretical basis for exact numerical computations of Hoenl-London factors for all types of spin-allowed electric dipole transitions in diatomic molecules. The computed Hoenl-London factors are then in the next step intended to be the basis for construction of synthetic molecular band spectra, with particular applications to upper atmosperic emissions (aurora)

Desorption of Cs+ ions with fast incident atomic and molecular ions

International Nuclear Information System (INIS)

Salehpour, M.; Hunt, J.E.; Tou, L.C.; Hedin, A.; Sundqvist, B.

1988-01-01

Preliminary results on desorption yield measurements of secondary Cs + ions, desorbed as a result of the impact of C + , O + , CO + , O 2 + , CO 2 + and C 4 H 9 + incident ions, in the energy range of 950 keV--3.5 MeV are presented. Molecular beams are found to give high yields of secondary Cs + as a result of impact of O 2 + compared to O + incident ions, indicate no ''collective'' molecular effects. 23 refs., 1 fig

The fundamentals of atomic and molecular physics

CERN Document Server

Brooks, Robert L

2013-01-01

The Fundamentals of Atomic and Molecular Physics is intended as an introduction to the field for advanced undergraduates who have taken quantum mechanics. Each chapter builds upon the previous, using the same tools and methods throughout. As the students progress through the book, their ability to use these tools will steadily increase, along with their confidence in their efficacy. The book treats the two-electron atom as the simplest example of the many-electron atom—as opposed to using techniques that are not applicable to many-electron atoms—so that it is unnecessary to develop additional equations when turning to multielectron atoms, such as carbon. External fields are treated using both perturbation theory and direct diagonalization and spontaneous emission is developed from first principles. Only diatomic molecules are considered with the hydrogen molecular ion and neutral molecule treated in some detail. This comprehensive coverage of the quantum mechanics of complex atoms and simple diatomic mole...

Diatom-Specific Oligosaccharide and Polysaccharide Structures Help to Unravel Biosynthetic Capabilities in Diatoms

Directory of Open Access Journals (Sweden)

Bruno Gügi

2015-09-01

Full Text Available Diatoms are marine organisms that represent one of the most important sources of biomass in the ocean, accounting for about 40% of marine primary production, and in the biosphere, contributing up to 20% of global CO2 fixation. There has been a recent surge in developing the use of diatoms as a source of bioactive compounds in the food and cosmetic industries. In addition, the potential of diatoms such as Phaeodactylum tricornutum as cell factories for the production of biopharmaceuticals is currently under evaluation. These biotechnological applications require a comprehensive understanding of the sugar biosynthesis pathways that operate in diatoms. Here, we review diatom glycan and polysaccharide structures, thus revealing their sugar biosynthesis capabilities.

Microwave quantum logic spectroscopy and control of molecular ions

DEFF Research Database (Denmark)

Shi, M.; F. Herskind, P.; Drewsen, M.

2013-01-01

the rotational state of a molecular ion and the electronic state of an atomic ion. In this setting, the atomic ion is used for read-out of the molecular ion state, in a manner analogous to quantum logic spectroscopy based on Raman transitions. In addition to high-precision spectroscopy, this setting allows...... for rotational ground state cooling, and can be considered as a candidate for the quantum information processing with polar molecular ions. All elements of our proposal can be realized with currently available technology....

Physics with fast molecular-ion beams

International Nuclear Information System (INIS)

Kanter, E.P.

1980-01-01

Fast (MeV) molecular-ion beams provide a unique source of energetic projectile nuclei which are correlated in space and time. The recognition of this property has prompted several recent investigations of various aspects of the interactions of these ions with matter. High-resolution measurements on the fragments resulting from these interactions have already yielded a wealth of new information on such diverse topics as plasma oscillations in solids and stereochemical structures of molecular ions as well as a variety of atomic collision phenomena. The general features of several such experiments will be discussed and recent results will be presented

Diatom Attachment at Aquatic Interfaces: Molecular Interactions, Mechanisms, and Physiology of Adhesion

National Research Council Canada - National Science Library

Gretz, Michael

1997-01-01

.... those more hydrophobic and that bacterial 'preconditioning' has variable effects on adhesion; (3) developed methodology for mass culture of fouling diatoms and isolation of adhesive components; (4...

Towards a representative periphytic diatom sample

Directory of Open Access Journals (Sweden)

2007-01-01

Full Text Available The need to acquire a representative periphytic diatom sample for river water quality monitoring has been recognised in the development of existing diatom indices, important in the development and employment of diatom monitoring tools for the Water Framework Directive. In this study, a nested design with replication is employed to investigate the magnitude of variation in diatom biomass, composition and Trophic Diatom Index at varying scales within a small chalk river. The study shows that the use of artificial substrates may not result in diatom communities that are typical of the surrounding natural substrates. Periphytic diatom biomass and composition varies between artificial and natural substrates, riffles and glides and between two stretches of the river channel. The study also highlights the existence of high variation in diatom frustule frequency and biovolume at the individual replicate scale which may have implications for the use of diatoms in routine monitoring.

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Czech Academy of Sciences Publication Activity Database

Bowler, Ch.; Allen, A. E.; Badger, J. H.; Grimwood, J.; Jabbari, K.; Kuo, A.; Maheswari, U.; Martens, C.; Maumus, F.; Otillar, R. P.; Rayko, E.; Salamov, A.; Vandepoele, K.; Beszteri, B.; Gruber, A.; Heijde, M.; Katinka, M.; Mock, T.; Valentin, K.; Verret, F.; Berges, J. A.; Brownlee, C.; Cadoret, J.-P.; Chiovitti, A.; Choi, Ch. J.; Coesel, S.; De Martino, A.; Detter, J. Ch.; Durkin, C.; Falciatore, A.; Fournet, J.; Haruta, M.; Huysman, M. J. J.; Jenkins, B. D.; Jiroutová, Kateřina; Jorgensen, R. E.; Joubert, Y.; Kaplan, A.; Kröger, N.; Kroth, P. G.; La Roche, J.; Lindquist, E.; Lommer, M.; Martin–Jézéquel, V.; Lopez, P. J.; Lucas, S.; Mangogna, M.; McGinnis, K.; Medlin, L. K.; Montsant, A.; Oudot–Le Secq, M.-P.; Napoli, C.; Oborník, Miroslav; Schnitzler Parker, M.; Petit, J.-L.; Porcel, B. M.; Poulsen, N.; Robison, M.; Rychlewski, L.; Rynearson, T. A.; Schmutz, J.; Shapiro, H.; Siaut, M.; Stanley, M.; Sussman, M. R.; Taylor, A. R.; Vardi, A.; von Dassow, P.; Vyverman, W.; Willis, A.; Wyrwicz, L. S.; Rokhsar, D. S.; Weissenbach, J.; Armbrust, E. V.; Green, B. R.; Van de Peer, Y.; Grigoriev, I. V.

2008-01-01

Roč. 456, 13-11-2008 (2008), s. 239-244 ISSN 0028-0836 Institutional research plan: CEZ:AV0Z60220518 Keywords : Phaeodactylum * genome * evolution * diatom Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 31.434, year: 2008

Environmental investigations using diatom microfossils

Science.gov (United States)

Smith, Kathryn E.L.; Flocks, James G.

2010-01-01

Diatoms are unicellular phytoplankton (microscopic plant-like organisms) with cell walls made of silica (called a frustule). They live in both freshwater and saltwater and can be found in just about every place on Earth that is wet. The shape and morphology of the diatom frustule unique to each species are used for identification. Due to the microscopic size of diatoms, high-power microscopy is required for diatom identification. Diatoms are vital to life on Earth. They are photosynthetic primary producers, using sunlight to create oxygen and organic carbon from carbon dioxide and water. They are a significant source of the oxygen we breathe, have a major impact on the global carbon cycle (Smetacek, 1999), and are a food source for many aquatic organisms (Mann, 1993). Diatom abundance has even been demonstrated to have an influence on the diversity of larger marine mammals, including whales (Marx and Uhen, 2010). Data on diatom abundance and diversity are extremely useful in environmental studies.

Transformation techniques for metabolic engineering of diatoms and haptophytes: current state and prospects.

Science.gov (United States)

Velmurugan, Natarajan; Deka, Deepi

2018-05-01

Diatoms and haptophytes represent a key segment of the dominant phytoplankton communities that frequently form massive blooms in the photic zone of the ocean and are considered indicators of global climate changes. Diatoms and haptophytes also play a vital role in the biological carbon fixation in the carbon cycles. Carbon partitioning within diatoms and haptophytes possesses a wide range of chemical compounds and storage materials, such as lipids, carbohydrates, and chlorophyll. Among the marine microorganisms, diatoms and haptophytes have been recognized as promising sources of long- and very long-chain polyunsaturated fatty acids (PUFA). So far, a variety of approaches have been employed for genetic modification in the nuclei of diatoms and haptophytes. Studies on transformation and metabolic engineering in various intracellular genomes, such as chloroplast and mitochondria, are scarce. Particle bombardment, Agrobacterium and PEG-mediated gene transfer, and electroporation have been reported for foreign gene transformation into the diatoms and haptophytes. Antibiotics (G418 and chloramphenicol) and herbicides (zeocin, hygromycin, and norflurazon) have been successfully demonstrated as the best selection markers. Despite the availability of a wide range of molecular tools for foreign gene expression in microalgae, very few promoters (lhcf1, nr, h4, ef2, fcp, and pds) have been reported for diatoms and haptophytes. Therefore, in this review, we first summarize the significant progress that has been achieved in transgene expression in diatoms and haptophytes and highlight the importance and availability of recently developed novel tools that are suitable for transgenic expression in diatoms and haptophytes.

Diatom Transcriptional and Physiological Responses to Changes in Iron Bioavailability across Ocean Provinces

Directory of Open Access Journals (Sweden)

Natalie R. Cohen

2017-11-01

Full Text Available Changes in iron (Fe bioavailability influence diatom physiology and community composition, and thus have a profound impact on primary productivity and ecosystem dynamics. Iron limitation of diatom growth rates has been demonstrated in both oceanic and coastal waters of the Northeast Pacific Ocean and is predicted to become more pervasive in future oceans. However, it is unclear how the strategies utilized by phytoplankton to cope with low Fe bioavailability and resupply differ across these ocean provinces. We investigated the response of diatom communities to variable Fe conditions through incubation experiments performed in the Fe mosaic of the California Upwelling Zone and along a natural Fe gradient in the Northeast Pacific Ocean. Through coupling gene expression of two dominant diatom taxa (Pseudo-nitzschia and Thalassiosira with biological rate process measurements, we provide an in-depth examination of the physiological and molecular responses associated with varying Fe status. Following Fe enrichment, oceanic diatoms showed distinct differential expression of gene products involved in nitrogen assimilation, photosynthetic carbon fixation, and vitamin production compared to diatoms from low-Fe coastal sites, possibly driven by the chronic nature of Fe stress at the oceanic site. Genes of interest involved in Fe and N metabolism additionally exhibited divergent expression patterns between the two diatom taxa investigated, demonstrating that diverse diatoms may invoke alternative strategies when dealing with identical changes in their environment. We report here several mechanisms used distinctly by coastal or oceanic diatom communities as well as numerous taxa-specific strategies for coping with Fe stress and rearranging nutrient metabolism following Fe enrichment.

Processing and characterization of diatom nanoparticles and microparticles as potential source of silicon for bone tissue engineering

Energy Technology Data Exchange (ETDEWEB)

Le, Thi Duy Hanh [Department of Industrial Engineering, University of Trento, Trento (Italy); BIOtech Research Center and European Institute of Excellence on Tissue Engineering and Regenerative Medicine, Trento (Italy); Bonani, Walter [Department of Industrial Engineering, University of Trento, Trento (Italy); BIOtech Research Center and European Institute of Excellence on Tissue Engineering and Regenerative Medicine, Trento (Italy); Interuniversity Consortium for Science and Technology of Materials, Trento Research Unit, Trento (Italy); Speranza, Giorgio [Center for Materials and Microsystems, PAM-SE, Fondazione Bruno Kessler, Trento (Italy); Sglavo, Vincenzo; Ceccato, Riccardo [Department of Industrial Engineering, University of Trento, Trento (Italy); Maniglio, Devid; Motta, Antonella [Department of Industrial Engineering, University of Trento, Trento (Italy); BIOtech Research Center and European Institute of Excellence on Tissue Engineering and Regenerative Medicine, Trento (Italy); Interuniversity Consortium for Science and Technology of Materials, Trento Research Unit, Trento (Italy); Migliaresi, Claudio, E-mail: claudio.migliaresi@unitn.it [Department of Industrial Engineering, University of Trento, Trento (Italy); BIOtech Research Center and European Institute of Excellence on Tissue Engineering and Regenerative Medicine, Trento (Italy); Interuniversity Consortium for Science and Technology of Materials, Trento Research Unit, Trento (Italy)

2016-02-01

Silicon plays an important role in bone formation and maintenance, improving osteoblast cell function and inducing mineralization. Often, bone deformation and long bone abnormalities have been associated with silica/silicon deficiency. Diatomite, a natural deposit of diatom skeleton, is a cheap and abundant source of biogenic silica. The aim of the present study is to validate the potential of diatom particles derived from diatom skeletons as silicon-donor materials for bone tissue engineering applications. Raw diatomite (RD) and calcined diatomite (CD) powders were purified by acid treatments, and diatom microparticles (MPs) and nanoparticles (NPs) were produced by fragmentation of purified diatoms under alkaline conditions. The influence of processing on the surface chemical composition of purified diatomites was evaluated by X-ray photoelectron spectroscopy (XPS). Diatoms NPs were also characterized in terms of morphology and size distribution by transmission electron microscopy (TEM) and Dynamic light scattering (DLS), while diatom MPs morphology was analyzed by scanning electron microscopy (SEM). Surface area and microporosity of the diatom particles were evaluated by nitrogen physisorption methods. Release of silicon ions from diatom-derived particles was demonstrated using inductively coupled plasma optical emission spectrometry (ICP/OES); furthermore, silicon release kinetic was found to be influenced by diatomite purification method and particle size. Diatom-derived microparticles (MPs) and nanoparticles (NPs) showed limited or no cytotoxic effect in vitro depending on the administration conditions. - Highlights: • Diatomite is a natural source of silica and has a potential as silicon-donor for bone regenerative applications. • Diatom particles derived from purified diatom skeletons were prepared by fragmentation under extreme alkaline condition. • Dissolution of diatom particles derived from diatom skeletons in DI water depend on purification method

High-precision laser and rf spectroscopy of atomic, molecular, and slow ion beams

International Nuclear Information System (INIS)

Childs, W.J.; Steimle, T.C.; Sen, A.; Azuma, Y.

1988-01-01

We have obtained extensive new structural information on the light diatomic radical ScO since the last report in this series. The new studies complete our systematic investigation of the fine and hyperfine structure (hfs) of the group IIIa monoxides LaO, YO, and ScO. The studies of the molecular X 2 Σ + electronic ground state were carried out using the molecular-beam laser-rf double-resonance method, and the excited electronic state information was obtained by complementing this data with Doppler-free laser fluorescence studies

Adiabatic Cooling for Rovibrational Spectroscopy of Molecular Ions

DEFF Research Database (Denmark)

Fisher, Karin

2017-01-01

The field of cold molecular ions is a fast growing one, with applications in high resolution spectroscopy and metrology, the search for time variations of fundamental constants, cold chemistry and collisions, and quantum information processing, to name a few. The study of single molecular ions...... is attractive as it enables one to push the limits of spectroscopic accuracy. Non-destructive spectroscopic detection of molecular ions can be achieved by co-trapping with an easier to detect atomic ion. The ion chain has coupled motion, and transitions which change both the internal and motional states...... to the measured heating rates, almost perfectly fitting existing heating rate theory. Further, the same model successfully predicted the heating rates of the in-phase mode of a two-ion crystal, indicating that we can use it to predict the heating rates in experiments on molecule-atom chains. Adiabatic cooling...

The iodine molecule insights into intra- and intermolecular perturbation in diatomic molecules

CERN Document Server

Lukashov, Sergey; Pravilov, Anatoly

2018-01-01

This book presents experimental and theoretical spectroscopic studies performed over the last 25 years on the iodine molecule’s excited states and their perturbations. It is going to be of interest to researchers who study intra- and intermolecular perturbations in diatomic molecules and more complex systems. The book offers a detailed treatment of the nonadiabatic perturbations of valence, ion pair and Rydberg states induced by intramolecular as well as intermolecular interactions in collisions or in weakly-bound complexes. It also provides an overview of current instrumentation and techniques as well as theoretical approaches describing intra- and intermolecular perturbations. The authors are experts in the use of spectroscopy for the study of intrinsic and collision-induced perturbations in diatomic iodine. They introduced new methods of two- and three-step optical population of the iodine ion-pair states. The iodine molecule has 23 valence states correlating with three dissociation limits, 20 so-called ...

The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism

Czech Academy of Sciences Publication Activity Database

Armbrust, E. V.; Berges, J. A.; Bowler, C.; Green, B. R.; Martinez, D.; Putnam, N. H.; Zhou, S.; Allen, A. E.; Apt, K. E.; Bechner, M.; Brzezinski, M. A.; Chaal, B. K.; Chiovitti, A.; Davis, A. K.; Demarest, M. S.; Detter, J. C.; Glavina, T.; Goodstein, D.; Hadi, M. Z.; Hellsten, U.; Hildebrand, M.; Jenkins, B. D.; Jurka, J.; Kapitonov, V. V.; Kröger, N.; Lau, W. W. Y.; Lane, T. W.; Larimer, F. W.; Lippmeier, J. C.; Lucas, S.; Medina, M.; Montsant, A.; Oborník, Miroslav; Schnitzler Parker, M.; Palenik, B.; Pazour, G. J.; Richardson, P. M.; Rynearson, T. A.; Saito, M. A.; Schwartz, D. C.; Thamatrakoln, K.; Valentin, K.; Vardi, A.; Wilkerson, F. P.; Rokhsar, D. S.

2004-01-01

Roč. 306, č. 5693 (2004), s. 79-86 ISSN 0036-8075 Institutional research plan: CEZ:AV0Z6022909 Keywords : diatom * genome * Thalassiosira Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 31.853, year: 2004

Electron Interference in Molecular Circular Polarization Attosecond XUV Photoionization

Directory of Open Access Journals (Sweden)

Kai-Jun Yuan

2015-01-01

Full Text Available Two-center electron interference in molecular attosecond photoionization processes is investigated from numerical solutions of time-dependent Schrödinger equations. Both symmetric H\\(_2^+\\ and nonsymmetric HHe\\(^{2+}\\ one electron diatomic systems are ionized by intense attosecond circularly polarized XUV laser pulses. Photoionization of these molecular ions shows signature of interference with double peaks (minima in molecular attosecond photoelectron energy spectra (MAPES at critical angles \\(\\vartheta_c\\ between the molecular \\(\\textbf{R}\\ axis and the photoelectron momentum \\(\\textbf{p}\\. The interferences are shown to be a function of the symmetry of electronic states and the interference patterns are sensitive to the molecular orientation and pulse polarization. Such sensitivity offers possibility for imaging of molecular structure and orbitals.

Molecular ions in comet tails

International Nuclear Information System (INIS)

Wyckoff, S.; Wehinger, P.A.

1976-01-01

Band intensities of the molecular ions CH + , CO + , N 2 + , and H 2 O + have been determined on an absolute scale from tail spectra of comet Kohoutek (1973f) and comet Bradfield (1974b). Photoionization and photodissociation rates have been computed for CH, CO, and N 2 . Also emission rate excitation g-factors for (1) photoionization plus excitation and (2) resonance fluorescence have been computed for the observed ions. It is shown that resonance fluorescence is the dominant excitation mechanism for observed comet tail ions at rapprox. =1 AU. Band system luminosities and molecular ion abundances within a projected nuclear distance rho 4 km have been determined for CH + , CO + , N 2 + , and H 2 O + in comet Kohoutek, and for H 2 O + in comet Bradfield. Estimates are also given for column densities of all observed ions at rhoapprox. =10 4 km on the tailward side of the coma. The observed H 2 O + column densities were found to be roughly the same in comet Kohoutek and comet Bradfield et equal heliocentric distances, while CO + was found to be approximately 100 times more abundant than H 2 O + , N 2 + , and CH + at rhoapprox. =10 4 km in comet Kohoutek. Finally, the relative abundances of the observed ions and of the presumed parent neutral species are briefly discussed

Diatom-inspired templates for 3D replication: natural diatoms versus laser written artificial diatoms

International Nuclear Information System (INIS)

Belegratis, M R; Schmidt, V; Nees, D; Stadlober, B; Hartmann, P

2014-01-01

The diatoms are ubiquitous, exist in large numbers and show a great diversity of features on their porous silica structures. Therefore, they inspire the fabrication of nanostructured templates for nanoimprint processes (NIL), where large structured areas with nanometer precision are required. In this study, two approaches regarding the respective challenges and potential exploitations are followed and discussed: the first one takes advantage of a template that is directly made of natural occurring diatoms. Here, two replication steps via soft lithography are needed to obtain a template which is subsequently used for NIL. The second approach exploits the technical capabilities of the precise 3D laser lithography (3DLL) based on two-photon polymerization of organic materials. This method enables the fabrication of arbitrary artificial diatom-inspired micro- and nanostructures and the design of an inverse structure. Therefore, only one replication step is needed to obtain a template for NIL. In both approaches, a replication technique for true 3D structures is shown. (paper)

Evolution and metabolic significance of the urea cycle in photosynthetic diatoms

Czech Academy of Sciences Publication Activity Database

Allen, A. E.; Dupont, Ch. L.; Oborník, Miroslav; Horák, Aleš; Nunes-Nesi, A.; McCrow, J. P.; Zheng, H.; Johnson, D. A.; Hu, H.; Fernie, A. R.; Bowler, Ch.

2011-01-01

Roč. 473, č. 7346 (2011), s. 203-209 ISSN 0028-0836 R&D Projects: GA ČR GA206/08/1423 Institutional research plan: CEZ:AV0Z60220518 Keywords : CARBAMOYL-PHOSPHATE SYNTHETASE * PHAEODACTYLUM-TRICORNUTUM * MAXIMUM-LIKELIHOOD * PHYLOGENETIC RECONSTRUCTION * MOLECULAR EVOLUTION * SEQUENCE ALIGNMENT * DIVERGENCE TIMES * MARINE DIATOMS * MIXED MODELS * TREE Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 36.280, year: 2011

Atomic and molecular physics with ion storage rings

International Nuclear Information System (INIS)

Larsson, M.

1995-01-01

Advances in ion-source, accelerator and beam-cooling technology have made it possible to produce high-quality beams of atomic ions in arbitrary charged states as well as molecular and cluster ions are internally cold. Ion beams of low emittance and narrow momentum spread are obtained in a new generation of ion storage-cooler rings dedicated to atomic and molecular physics. The long storage times (∼ 5 s ≤ τ ≤ days) allow the study of very slow processes occurring in charged (positive and negative) atoms, molecules and clusters. Interactions of ions with electrons and/or photons can be studied by merging the stored ion beam with electron and laser beams. The physics of storage rings spans particles having a charge-to-mass ratio ranging from 60 + and C 70 + ) to 0.4 - 1.0 (H + , D + , He 2+ , ..., U 92+ ) and collision processes ranging from <1 meV to ∼ 70 GeV. It incorporates, in addition to atomic and molecular physics, tests of fundamental physics theories and atomic physics bordering on nuclear and chemical physics. This exciting development concerning ion storage rings has taken place within the last five to six years. (author)

Complex dynamics in diatomic molecules. Part II: Quantum trajectories

International Nuclear Information System (INIS)

Yang, C.-D.; Weng, H.-J.

2008-01-01

The second part of this paper deals with quantum trajectories in diatomic molecules, which has not been considered before in the literature. Morse potential serves as a more accurate function than a simple harmonic oscillator for illustrating a realistic picture about the vibration of diatomic molecules. However, if we determine molecular dynamics by integrating the classical force equations derived from a Morse potential, we will find that the resulting trajectories do not consist with the probabilistic prediction of quantum mechanics. On the other hand, the quantum trajectory determined by Bohmian mechanics [Bohm D. A suggested interpretation of the quantum theory in terms of hidden variable. Phys. Rev. 1952;85:166-179] leads to the conclusion that a diatomic molecule is motionless in all its vibrational eigen-states, which also contradicts probabilistic prediction of quantum mechanics. In this paper, we point out that the quantum trajectory of a diatomic molecule completely consistent with quantum mechanics does exist and can be solved from the quantum Hamilton equations of motion derived in Part I, which is based on a complex-space formulation of fractal spacetime [El Naschie MS. A review of E-Infinity theory and the mass spectrum of high energy particle physics. Chaos, Solitons and Fractals 2004;19:209-36; El Naschie MS. E-Infinity theory - some recent results and new interpretations. Chaos, Solitons and Fractals 2006;29:845-853; El Naschie MS. The concepts of E-infinity. An elementary introduction to the cantorian-fractal theory of quantum physics. Chaos, Solitons and Fractals 2004;22:495-511; El Naschie MS. SU(5) grand unification in a transfinite form. Chaos, Solitons and Fractals 2007;32:370-374; Nottale L. Fractal space-time and microphysics: towards a theory of scale relativity. Singapore: World Scientific; 1993; Ord G. Fractal space time and the statistical mechanics of random works. Chaos, Soiltons and Fractals 1996;7:821-843] approach to quantum

Improved abundance sensitivity of molecular ions in positive-ion APCI MS analysis of petroleum in toluene.

Science.gov (United States)

Kim, Young Hwan; Kim, Sunghwan

2010-03-01

Positive-ion atmospheric pressure chemical ionization (APCI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analyses of petroleum sample were performed with higher sensitivity by switching the solvent composition from toluene and methanol or acetonitrile to a one-component system consisting only of toluene. In solvent blends, molecular ions were more abundant than were protonated ions with increasing percentages of toluene. In 100% toluene, the double-bond equivalence (DBE) distributions of molecular ions obtained by APCI MS for each compound class were very similar to those obtained in dopant assisted atmospheric pressure photo ionization (APPI) MS analyses. Therefore, it was concluded that charge-transfer reaction, which is important in toluene-doped APPI processes, also plays a major role in positive-ion APCI. In the DBE distributions of S(1), S(2), and SO heteroatom classes, a larger enhancement in the relative abundance of molecular ions at fairly specific DBE values was observed as the solvent was progressively switched to toluene. This enhanced abundance of molecular ions was likely dependent on molecular structure. Copyright 2010 American Society for Mass Spectrometry. Published by Elsevier Inc. All rights reserved.

Transparent Exopolymeric Particles (TEP Selectively Increase Biogenic Silica Dissolution From Fossil Diatoms as Compared to Fresh Diatoms

Directory of Open Access Journals (Sweden)

Jordan Toullec

2018-03-01

Full Text Available Diatom production is mainly supported by the dissolution of biogenic silica (bSiO2 within the first 200 m of the water column. The upper oceanic layer is enriched in dissolved and/or colloidal organic matter, such as exopolymeric polysaccharides (EPS and transparent exopolymeric particles (TEP excreted by phytoplankton in large amounts, especially at the end of a bloom. In this study we explored for the first time the direct influence of TEP-enriched diatom excretions on bSiO2 dissolution. Twelve dissolution experiments on fresh and fossil diatom frustules were carried out on seawater containing different concentrations of TEP extracted from diatom cultures. Fresh diatom frustules were cleaned from the organic matter by low ash temperature, and fossil diatoms were made from diatomite powder. Results confirm that newly formed bSiO2 dissolved at a faster rate than fossil diatoms due to a lower aluminum (Al content. Diatom excretions have no effect on the dissolution of the newly formed bSiO2 from Chaetoceros muelleri. Reversely, the diatomite specific dissolution rate constant and solubility of the bSiO2 were positively correlated to TEP concentrations, suggesting that diatom excretion may provide an alternative source of dSi when limitations arise.

An ion cooling and state characterization apparatus for studies of molecular ion dissociative interactions

International Nuclear Information System (INIS)

Deng, Shihu; Vane, C R; Bannister, M E; Havener, C C; Meyer, F W; Krause, H F; Hettich, R L; Goeringer, D E; Van Berkel, G J

2009-01-01

An experimental capability is being developed at the Oak Ridge National Laboratory Multi-Charged Ion Research Facility (ORNL MIRF) to enable stored cooling and state characterization of molecular ions of essentially any mass. Ions selected from a variety of available sources are injected from the side into a 1.5 meter long electrostatic mirror trap, where excited internal states are cooled by radiative cooling. An electron beam target located near the middle of the ion-trap region, coupled with neutral fragment imaging detector systems at each end of the trap, permits state-specific studies of electron-molecular ion dissociation.

Comparison of single-ion molecular dynamics in common solvents

Science.gov (United States)

Muralidharan, A.; Pratt, L. R.; Chaudhari, M. I.; Rempe, S. B.

2018-06-01

Laying a basis for molecularly specific theory for the mobilities of ions in solutions of practical interest, we report a broad survey of velocity autocorrelation functions (VACFs) of Li+ and PF6- ions in water, ethylene carbonate, propylene carbonate, and acetonitrile solutions. We extract the memory function, γ(t), which characterizes the random forces governing the mobilities of ions. We provide comparisons controlling for the effects of electrolyte concentration and ion-pairing, van der Waals attractive interactions, and solvent molecular characteristics. For the heavier ion (PF6-), velocity relaxations are all similar: negative tail relaxations for the VACF and a clear second relaxation for γ (t ), observed previously also for other molecular ions and with n-pentanol as the solvent. For the light Li+ ion, short time-scale oscillatory behavior masks simple, longer time-scale relaxation of γ (t ). But the corresponding analysis of the solventberg Li+(H2O)4 does conform to the standard picture set by all the PF6- results.

Novel sex cells and evidence for sex pheromones in diatoms.

Science.gov (United States)

Sato, Shinya; Beakes, Gordon; Idei, Masahiko; Nagumo, Tamotsu; Mann, David G

2011-01-01

Diatoms belong to the stramenopiles, one of the largest groups of eukaryotes, which are primarily characterized by a presence of an anterior flagellum with tubular mastigonemes and usually a second, smooth flagellum. Based on cell wall morphology, diatoms have historically been divided into centrics and pennates, of which only the former have flagella and only on the sperm. Molecular phylogenies show the pennates to have evolved from among the centrics. However, the timing of flagellum loss--whether before the evolution of the pennate lineage or after--is unknown, because sexual reproduction has been so little studied in the 'araphid' basal pennate lineages, to which Pseudostaurosira belongs. Sexual reproduction of an araphid pennate, Pseudostaurosira trainorii, was studied with light microscopy (including time lapse observations and immunofluorescence staining observed under confocal scanning laser microscopy) and SEM. We show that the species produces motile male gametes. Motility is mostly associated with the extrusion and retrieval of microtubule-based 'threads', which are structures hitherto unknown in stramenopiles, their number varying from one to three per cell. We also report experimental evidence for sex pheromones that reciprocally stimulate sexualization of compatible clones and orientate motility of the male gametes after an initial 'random walk'. The threads superficially resemble flagella, in that both are produced by male gametes and contain microtubules. However, one striking difference is that threads cannot beat or undulate and have no motility of their own, and they do not bear mastigonemes. Threads are sticky and catch and draw objects, including eggs. The motility conferred by the threads is probably crucial for sexual reproduction of P. trainorii, because this diatom is non-motile in its vegetative stage but obligately outbreeding. Our pheromone experiments are the first studies in which gametogenesis has been induced in diatoms by cell

Mean excitation energies for molecular ions

Energy Technology Data Exchange (ETDEWEB)

Jensen, Phillip W.K.; Sauer, Stephan P.A. [Department of Chemistry, University of Copenhagen, Copenhagen (Denmark); Oddershede, Jens [Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense (Denmark); Quantum Theory Project, Departments of Physics and Chemistry, University of Florida, Gainesville, FL (United States); Sabin, John R., E-mail: sabin@qtp.ufl.edu [Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense (Denmark); Quantum Theory Project, Departments of Physics and Chemistry, University of Florida, Gainesville, FL (United States)

2017-03-01

The essential material constant that determines the bulk of the stopping power of high energy projectiles, the mean excitation energy, is calculated for a range of smaller molecular ions using the RPA method. It is demonstrated that the mean excitation energy of both molecules and atoms increase with ionic charge. However, while the mean excitation energies of atoms also increase with atomic number, the opposite is the case for mean excitation energies for molecules and molecular ions. The origin of these effects is explained by considering the spectral representation of the excited state contributing to the mean excitation energy.

Understanding Molecular-Ion Neutral Atom Collisions for the Production of Ultracold Molecular Ions

Science.gov (United States)

2014-02-03

SECURITY CLASSIFICATION OF: This project was superseded and replaced by another ARO-funded project of the same name, which is still continuing. The goal...cooled atoms," IOTA -COST Workshop on molecular ions, Arosa, Switzerland. 5. E.R. Hudson, "Sympathetic cooling of molecules with laser cooled

New formula for dependence of molecular electronic energy on internuclear distance

International Nuclear Information System (INIS)

Rebane, T.K.

1988-01-01

We formulate an integral virial theorem which connects the change in the molecular electronic energy during finite changes in the size of the nuclear core (in the case of a diatomic molecule, during finite changes of the internuclear distance) with a matrix element of the kinetic electronic energy operator and with an overlap integral between wave functions. Our results can be used to calculate the dependence of the molecular electronic energy on the internuclear distance, as well as to check the quality of, and to improve, the approximate electronic wave functions. The theory is illustrated by the simplest example of the approximate MO LCAO wave function for the hydrogen molecular ion

Dynamics of molecular superrotors in an external magnetic field

Science.gov (United States)

Korobenko, Aleksey; Milner, Valery

2015-08-01

We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.

Recent work with fast molecular-ion beams at Argonne National Laboratory

International Nuclear Information System (INIS)

Cooney, P.J.; Gemmell, D.S.; Groeneveld, K.O.; Kanter, E.P.; Pietsch, W.J.; Vager, Z.; Zabransky, B.J.

1979-01-01

Research in these areas during 1979 is summarized: (a) studies of molecular-ion dissociation in gaseous targets, (b) developing an understanding of the origins of central peaks and of the two phenomena of the transmission of fast molecular ions through thin foil targets and of the production of neutral fragments from collision-induced dissociation of fast molecular projectiles, (c) studies exploring the extent to which high-resolution measurements on dissociation fragments can be used to determine the stereochemical structures of the molecular ions in the incident beam, (d) extensive modifications to the beam-line and apparatus at the 4-MV Dynamitron so as to permit a wide variety of coincidence measurements on fragments from collision-induced molecular-ion dissociation

Evolutionary origins and functions of the carotenoid biosynthetic pathway in marine diatoms

Czech Academy of Sciences Publication Activity Database

Coesel, S.; Oborník, Miroslav; Varela, J.; Falciatore, A.; Bowler, C.

2008-01-01

Roč. 3, č. 8 (2008), s. 1-16 E-ISSN 1932-6203 R&D Projects: GA AV ČR IAA500220502 Institutional research plan: CEZ:AV0Z60220518 Keywords : marine diatoms * carotenoid pathway * evolution Subject RIV: EB - Genetics ; Molecular Biology

Luminescence properties of a nanoporous freshwater diatom.

Science.gov (United States)

Goswami, Bondita; Choudhury, Amarjyoti; Buragohain, Alak K

2012-01-01

Freshwater diatom frustules show special optical properties. In this paper we observed luminescence properties of the freshwater diatom Cyclotella meneghiniana. To confirm the morphological properties we present scanning electron microscopy (SEM) images. X-ray diffraction (XRD) studies were carried out to visualize the structural properties of the frustules, confirming that silica present in diatom frustules crystallizes in an α-quartz structure. Study of the optical properties of the silica frustules of diatoms using ultra-violet-visible (UV-vis) spectroscopy and photoluminescence spectroscopy confirmed that the diatom C. meneghiniana shows luminescence in the blue region of the electromagnetic spectrum when irradiated with UV light. This property of diatoms can be exploited to obtain many applications in day-to-day life. Also, using time-resolved photoluminescence spectroscopy (TRPL) it was confirmed that this species of diatom shows bi-exponential decay. Copyright © 2011 John Wiley & Sons, Ltd.

Amorphous molecular junctions produced by ion irradiation on carbon nanotubes

International Nuclear Information System (INIS)

Wang Zhenxia; Yu Liping; Zhang Wei; Ding Yinfeng; Li Yulan; Han Jiaguang; Zhu Zhiyuan; Xu Hongjie; He Guowei; Chen Yi; Hu Gang

2004-01-01

Experiments and molecular dynamics have demonstrated that electron irradiation could create molecular junctions between crossed single-wall carbon nanotubes. Recently molecular dynamics computation predicted that ion irradiation could also join single-walled carbon nanotubes. Employing carbon ion irradiation on multi-walled carbon nanotubes, we find that these nanotubes evolve into amorphous carbon nanowires, more importantly, during the process of which various molecular junctions of amorphous nanowires are formed by welding from crossed carbon nanotubes. It demonstrates that ion-beam irradiation could be an effective way not only for the welding of nanotubes but also for the formation of nanowire junctions

Geometric and electronic structures of molecular ions from high energy collisions

International Nuclear Information System (INIS)

Groeneveld, K.O.

1983-01-01

This chapter examines the characteristics of heavy ion collision and of beam foil spectroscopy. It discusses the kinematic consequences of the high energies and presents results from ''Coulomb explosion'' and structure determination of molecular ions. It demonstrates that studies of molecular ions with accelerators can provide electronic and geometric structure information of molecules or molecular ions and points out that the understanding of the microscopic processes at such high energies is incomplete and needs further experimental and theoretical efforts

Tryptophan biosynthesis in stramenopiles: eukaryotic winners in the diatom complex chloroplast

Czech Academy of Sciences Publication Activity Database

Jiroutová, Kateřina; Horák, Aleš; Bowler, C.; Oborník, Miroslav

2007-01-01

Roč. 65, č. 5 (2007), s. 496-511 ISSN 0022-2844 R&D Projects: GA AV ČR IAA500220502 Institutional research plan: CEZ:AV0Z60220518 Keywords : tryptophan synthesis * mosaic origin * diatom * Oomycetes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.234, year: 2007

Quantum logic for the control and manipulation of molecular ions using a frequency comb

International Nuclear Information System (INIS)

Ding, S; Matsukevich, D N

2012-01-01

We propose a scheme for the preparation, manipulation and detection of quantum states of single molecular ions. In this scheme, molecular and atomic ions are confined in radio-frequency Paul trap and share common modes of motion. A frequency comb laser field is used to drive stimulated Raman transitions that couple internal states of the molecular ion with the motion of ions. State transfer from the molecular ion to the atomic ion via the common mode of motion results in efficient state detection for the molecule. The coupling of molecular states to the motion and the subsequent sideband cooling of the ions provide a way to prepare the molecular ion in a well-defined state. (paper)

Diatoms from a peat bog on the Pešter plateau (southwestern Serbia: New records for diatom flora of Serbia

Directory of Open Access Journals (Sweden)

Vidaković Danijela

2016-01-01

Full Text Available The distribution of diatoms was studied in three types of diatom communities (epiphytes, benthos and plankton of a peat bog on the Pešter plateau. The observed diatom flora inhabited all investigated communities, comprising in total 250 taxa in 53 genera. Among them, 45 taxa were new records for the Serbian diatom flora. Identified taxa belonged to different groups of algae, however alkaliphile diatoms were dominant. New ecological data for Encyonopsis minuta, Pinnularia isostauron and P. marchica are presented here. All the diatoms were documented by light micrographs, and brief notes on their morphology, distribution and ecology are provided. [Projekat Ministarstva nauke Republike Srbije, br. TR 037009

Toward precise potential energy curves for diatomic molecules, derived from experimental line positions

International Nuclear Information System (INIS)

Helm, H.

1984-01-01

An inverted, first-order perturbation approach is used to derive potential energy curves for diatomic molecules from experimental line positions of molecular bands. The concept adopted here is based on the inverted perturbation analysis (IPA) proposed by Kozman and Hinze, but uses radial eigenfunctions of the trial potential energy curves as basis sets for the perturbation correction. Using molecular linepositions rather than molecular energy levels we circumvent the necessity of defining molecular constants for the molecule prior to the derivation of the potential energy curves. (Author)

Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions

Science.gov (United States)

Choi, Jun-Ho; Lee, Hochan; Choi, Hyung Ran; Cho, Minhaeng

2018-04-01

In molecular and cellular biology, dissolved ions and molecules have decisive effects on chemical and biological reactions, conformational stabilities, and functions of small to large biomolecules. Despite major efforts, the current state of understanding of the effects of specific ions, osmolytes, and bioprotecting sugars on the structure and dynamics of water H-bonding networks and proteins is not yet satisfactory. Recently, to gain deeper insight into this subject, we studied various aggregation processes of ions and molecules in high-concentration salt, osmolyte, and sugar solutions with time-resolved vibrational spectroscopy and molecular dynamics simulation methods. It turns out that ions (or solute molecules) have a strong propensity to self-assemble into large and polydisperse aggregates that affect both local and long-range water H-bonding structures. In particular, we have shown that graph-theoretical approaches can be used to elucidate morphological characteristics of large aggregates in various aqueous salt, osmolyte, and sugar solutions. When ion and molecular aggregates in such aqueous solutions are treated as graphs, a variety of graph-theoretical properties, such as graph spectrum, degree distribution, clustering coefficient, minimum path length, and graph entropy, can be directly calculated by considering an ensemble of configurations taken from molecular dynamics trajectories. Here we show percolating behavior exhibited by ion and molecular aggregates upon increase in solute concentration in high solute concentrations and discuss compelling evidence of the isomorphic relation between percolation transitions of ion and molecular aggregates and water H-bonding networks. We anticipate that the combination of graph theory and molecular dynamics simulation methods will be of exceptional use in achieving a deeper understanding of the fundamental physical chemistry of dissolution and in describing the interplay between the self-aggregation of solute

Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions.

Science.gov (United States)

Choi, Jun-Ho; Lee, Hochan; Choi, Hyung Ran; Cho, Minhaeng

2018-04-20

In molecular and cellular biology, dissolved ions and molecules have decisive effects on chemical and biological reactions, conformational stabilities, and functions of small to large biomolecules. Despite major efforts, the current state of understanding of the effects of specific ions, osmolytes, and bioprotecting sugars on the structure and dynamics of water H-bonding networks and proteins is not yet satisfactory. Recently, to gain deeper insight into this subject, we studied various aggregation processes of ions and molecules in high-concentration salt, osmolyte, and sugar solutions with time-resolved vibrational spectroscopy and molecular dynamics simulation methods. It turns out that ions (or solute molecules) have a strong propensity to self-assemble into large and polydisperse aggregates that affect both local and long-range water H-bonding structures. In particular, we have shown that graph-theoretical approaches can be used to elucidate morphological characteristics of large aggregates in various aqueous salt, osmolyte, and sugar solutions. When ion and molecular aggregates in such aqueous solutions are treated as graphs, a variety of graph-theoretical properties, such as graph spectrum, degree distribution, clustering coefficient, minimum path length, and graph entropy, can be directly calculated by considering an ensemble of configurations taken from molecular dynamics trajectories. Here we show percolating behavior exhibited by ion and molecular aggregates upon increase in solute concentration in high solute concentrations and discuss compelling evidence of the isomorphic relation between percolation transitions of ion and molecular aggregates and water H-bonding networks. We anticipate that the combination of graph theory and molecular dynamics simulation methods will be of exceptional use in achieving a deeper understanding of the fundamental physical chemistry of dissolution and in describing the interplay between the self-aggregation of solute

Molecular Ions in Ion Upflows and their Effects on Hot Atomic Oxygen Production

Science.gov (United States)

Foss, V.; Yau, A. W.; Shizgal, B.

2017-12-01

We present new direct ion composition observations of molecular ions in auroral ion upflows from the CASSIOPE Enhanced Polar Outflow Probe (e-POP). These observed molecular ions are N2+, NO+, and possibly O2+, and are found to occur at all e-POP altitudes starting at about 400 km, during auroral substorms and the different phases of magnetic storms, sometimes with upflow velocities exceeding a few hundred meters per second and abundances of 5-10%. The dissociative recombination of both O2+ and NO+ was previously proposed as an important source of hot oxygen atoms in the topside thermosphere [Hickey et al., 1995]. We investigate the possible effect of the observed molecular ions on the production of hot oxygen atoms in the storm and substorm-time auroral thermosphere. We present numerical solutions of the Boltzmann equation for the steady-state oxygen energy distribution function, taking into account both the production of the hot atoms and their subsequent collisional relaxation. Our result suggests the formation of a hot oxygen population with a characteristic temperature on the order of 0.3 eV and constituting 1-5% of the oxygen density near the exobase. We discuss the implication of this result in the context of magnetosphere-ionosphere-thermosphere coupling.

Nonlinear quantum dynamics in diatomic molecules: Vibration, rotation and spin

International Nuclear Information System (INIS)

Yang, Ciann-Dong; Weng, Hung-Jen

2012-01-01

Highlights: ► This paper reveals the internal nonlinear dynamics embedded in a molecular quantum state. ► Analyze quantum molecular dynamics in a deterministic way, while preserving the consistency with probability interpretation. ► Molecular vibration–rotation interaction and spin–orbital coupling are considered simultaneously. ► Spin is just the remnant angular motion when orbital angular momentum is zero. ► Spin is the “zero dynamics” of nonlinear quantum dynamics. - Abstract: For a given molecular wavefunction Ψ, the probability density function Ψ ∗ Ψ is not the only information that can be extracted from Ψ. We point out in this paper that nonlinear quantum dynamics of a diatomic molecule, completely consistent with the probability prediction of quantum mechanics, does exist and can be derived from the quantum Hamilton equations of motion determined by Ψ. It can be said that the probability density function Ψ ∗ Ψ is an external representation of the quantum state Ψ, while the related Hamilton dynamics is an internal representation of Ψ, which reveals the internal mechanism underlying the externally observed random events. The proposed internal representation of Ψ establishes a bridge between nonlinear dynamics and quantum mechanics, which allows the methods and tools already developed by the former to be applied to the latter. Based on the quantum Hamilton equations of motion derived from Ψ, vibration, rotation and spin motions of a diatomic molecule and the interactions between them can be analyzed simultaneously. The resulting dynamic analysis of molecular motion is compared with the conventional probability analysis and the consistency between them is demonstrated.

Novel sex cells and evidence for sex pheromones in diatoms.

Directory of Open Access Journals (Sweden)

Shinya Sato

Full Text Available BACKGROUND: Diatoms belong to the stramenopiles, one of the largest groups of eukaryotes, which are primarily characterized by a presence of an anterior flagellum with tubular mastigonemes and usually a second, smooth flagellum. Based on cell wall morphology, diatoms have historically been divided into centrics and pennates, of which only the former have flagella and only on the sperm. Molecular phylogenies show the pennates to have evolved from among the centrics. However, the timing of flagellum loss--whether before the evolution of the pennate lineage or after--is unknown, because sexual reproduction has been so little studied in the 'araphid' basal pennate lineages, to which Pseudostaurosira belongs. METHODS/PRINCIPAL FINDING: Sexual reproduction of an araphid pennate, Pseudostaurosira trainorii, was studied with light microscopy (including time lapse observations and immunofluorescence staining observed under confocal scanning laser microscopy and SEM. We show that the species produces motile male gametes. Motility is mostly associated with the extrusion and retrieval of microtubule-based 'threads', which are structures hitherto unknown in stramenopiles, their number varying from one to three per cell. We also report experimental evidence for sex pheromones that reciprocally stimulate sexualization of compatible clones and orientate motility of the male gametes after an initial 'random walk'. CONCLUSIONS/SIGNIFICANCE: The threads superficially resemble flagella, in that both are produced by male gametes and contain microtubules. However, one striking difference is that threads cannot beat or undulate and have no motility of their own, and they do not bear mastigonemes. Threads are sticky and catch and draw objects, including eggs. The motility conferred by the threads is probably crucial for sexual reproduction of P. trainorii, because this diatom is non-motile in its vegetative stage but obligately outbreeding. Our pheromone experiments

Dynamics of molecular superrotors in an external magnetic field

International Nuclear Information System (INIS)

Korobenko, Aleksey; Milner, Valery

2015-01-01

We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin–rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation. (paper)

Theoretical study of quantum molecular reaction dynamics and of the effects of intense laser radiation on a diatomic molecule

International Nuclear Information System (INIS)

Dardi, P.S.

1984-11-01

Within the very broad field of molecular dynamics, we have concentrated on two simple yet important systems. The systems are simple enough so that they are adequately described with a single Born-Oppenheimer potential energy surface and that the dynamics can be calculated accurately. They are important because they give insight into solving more complicated systems. First we discuss H + H 2 reactive scattering. We present an exact formalism for atom-diatom reactive scattering which avoids the problem of finding a coordinate system appropriate for both reactants and products. We present computational results for collinear H + H 2 reactive scattering which agree very well with previous calculations. We also present a coupled channel distorted wave Born approximation for atom-diatom reactive scattering which we show is a first order approximation to our exact formalism. We present coupled channel DWBA results for three dimensional H + H 2 reactive scattering. The second system is an isolated HF molecule in an intense laser field. Using classical trajectories and quantum dynamics, we look at energy absorbed and transition probabilities as a function of the laser pulse time and also averaged over the pulse time. Calculations are performed for both rotating and nonrotating HF. We examine one and two photon absorption about the fundamental frequency, multiphoton absorption, and overtone absorption. 127 references, 31 figures, 12 tables

Theoretical study of quantum molecular reaction dynamics and of the effects of intense laser radiation on a diatomic molecule

Energy Technology Data Exchange (ETDEWEB)

Dardi, P.S.

1984-11-01

Within the very broad field of molecular dynamics, we have concentrated on two simple yet important systems. The systems are simple enough so that they are adequately described with a single Born-Oppenheimer potential energy surface and that the dynamics can be calculated accurately. They are important because they give insight into solving more complicated systems. First we discuss H + H/sub 2/ reactive scattering. We present an exact formalism for atom-diatom reactive scattering which avoids the problem of finding a coordinate system appropriate for both reactants and products. We present computational results for collinear H + H/sub 2/ reactive scattering which agree very well with previous calculations. We also present a coupled channel distorted wave Born approximation for atom-diatom reactive scattering which we show is a first order approximation to our exact formalism. We present coupled channel DWBA results for three dimensional H + H/sub 2/ reactive scattering. The second system is an isolated HF molecule in an intense laser field. Using classical trajectories and quantum dynamics, we look at energy absorbed and transition probabilities as a function of the laser pulse time and also averaged over the pulse time. Calculations are performed for both rotating and nonrotating HF. We examine one and two photon absorption about the fundamental frequency, multiphoton absorption, and overtone absorption. 127 references, 31 figures, 12 tables.

Electron-vibrational transitions under molecular ions collisions with slow electrons

International Nuclear Information System (INIS)

Andreev, E.A.

1993-01-01

A concept of a multichannel quantum defect is considered and basic theoretic ratios of inelastic collisional processes with the participation of molecular positive ions and slow electrons playing an important role both in atmospheric and laboratory plasma, are presented. The problem of scattering channel number limitation with the provision of S-matrix unique character is considered. Different models of electron rotation-vibrational connection under collision of two-atom molecular ions with slow electrons are analysed. Taking N 2 + as an example, a high efficiency of transitions between different electron states of a molecular ion is shown. 73 refs., 9 figs., 1 tab

Non-destructive state detection for quantum logic spectroscopy of molecular ions.

Science.gov (United States)

Wolf, Fabian; Wan, Yong; Heip, Jan C; Gebert, Florian; Shi, Chunyan; Schmidt, Piet O

2016-02-25

Precision laser spectroscopy of cold and trapped molecular ions is a powerful tool in fundamental physics--used, for example, in determining fundamental constants, testing for their possible variation in the laboratory, and searching for a possible electric dipole moment of the electron. However, the absence of cycling transitions in molecules poses a challenge for direct laser cooling of the ions, and for controlling and detecting their quantum states. Previously used state-detection techniques based on photodissociation or chemical reactions are destructive and therefore inefficient, restricting the achievable resolution in laser spectroscopy. Here, we experimentally demonstrate non-destructive detection of the quantum state of a single trapped molecular ion through its strong Coulomb coupling to a well controlled, co-trapped atomic ion. An algorithm based on a state-dependent optical dipole force changes the internal state of the atom according to the internal state of the molecule. We show that individual quantum states in the molecular ion can be distinguished by the strength of their coupling to the optical dipole force. We also observe quantum jumps (induced by black-body radiation) between rotational states of a single molecular ion. Using the detuning dependence of the state-detection signal, we implement a variant of quantum logic spectroscopy of a molecular resonance. Our state-detection technique is relevant to a wide range of molecular ions, and could be applied to state-controlled quantum chemistry and to spectroscopic investigations of molecules that serve as probes for interstellar clouds.

Use of molecular ion beams from a tandem accelerator

International Nuclear Information System (INIS)

Faibis, A.; Goldring, G.; Hass, M.; Kaim, R.; Plesser, I.; Vager, Z.

1981-01-01

A large variety of positive molecular ion beams can be produced by gaseous charge exchange in the terminal of a tandem accelerator. After acceleration the molecules are usually dissociated by passage through a thin foil. Measurements of the break-up products provide a way to study both the structure of incident ions and the effects of electronic potentials on the internuclear interaction inside the foil. Beam intensities of a few picoamperes are quite adequate for these measurements, and the relatively high energy obtained by use of a tandem accelerator has the advantage of minimizing multiple scattering effects in the foil. The main difficulty in using the molecular beams lies in the large magnetic rigidity of singly-charged heavy molecular ions

Sampler collection gadget for epilithic diatoms.

Science.gov (United States)

Salomoni, S E; Torgan, L C; Rocha, O

2007-11-01

This work present a new gadget for sampling epilithic diatoms from both lentic and lotic enviroments. The sampler consists of a polystyrene cylinder, left to float on the surface of the water, to which stone substrates are attached. This epilithic diatom sampler (EDS) can be used to detect spatial and temporal richness and density variation in the study of the diatom community, as well as in water quality monitoring.

Resonant ion-pair formation in electron collisions with HD+ and OH+

International Nuclear Information System (INIS)

Larson, Aa.; Djuric, N.; Zong, W.; Greene, C. H.; Orel, A. E.; Al-Khalili, A.; Derkatch, A. M.; Le Padellec, A.; Neau, A.; Rosen, S.

2000-01-01

Resonant ion-pair formation from collisions of electrons with electronic and vibronic ground-state diatomic molecular ions has been studied in the present work for HD + and OH + . The cross section for HD + has a magnitude of the order of 3x10 -19 cm 2 and is characterized by an energy threshold and 14 resolved peaks in the energy range up to 16 eV. A theoretical study confirms that the structures derive primarily from quantum interference of the multiple dissociation pathways. Measurements for OH + reveal that the cross section for H + and O - formation is lower than 10 -21 cm 2 at energies of 6 and 12 eV. (c) 2000 The American Physical Society

Isolation and Characterization of Silaffin that Catalyze Biosilica Formation from Marine Diatom Chaetoceros gracilis

Directory of Open Access Journals (Sweden)

AGNES IMELDA MANURUNG

2007-09-01

Full Text Available The method of making silica in industries requires extreme conditions. The finding of proteins involved in the formation of biosilica from diatoms, has opened up an alternative way of production. Chaetoceros gracilis is one of the diatoms, which is potential in producing silaffin protein. This study aimed to isolate and to characterize the protein. We also analyzed the protein activity toward tetraethoxyorthosilicate (TEOS substrate in in vitro reaction. Diatom biomass was harvested and further kept in 2% SDS/100 mM EDTA solution. Protein isolation was conducted by dissolving the silica and separating the protein by soaking in 2 M HF/8 M NH4F. Protein concentration was analyzed using Bradford method and the molecular weight was estimated through SDS-PAGE. Protein activity was observed by reacting it with TEOS substrate to form silica polymer and measured by colorimetric molibdate assay. Protein concentration was 1.20 mg/ml and appeared filamentous. The apparent molecular weights consisted of 12, 23, 42, 44 kDa. These protein was able to polymerize the silica at room temperature within 10 min. As much as 85.65 μmol TEOS was polymerized per 1.4 × 106 silaffin protein per min. SEM analysis showed the formation of spherical, aggregate biosilica.

Isolation and Characterization of Silaffin that Catalyze Biosilica Formation from Marine Diatom Chaetoceros gracilis

Directory of Open Access Journals (Sweden)

AGNES IMELDA MANURUNG

2007-09-01

Full Text Available The method of making silica in industries requires extreme conditions. The finding of proteins involved in the formation of biosilica from diatoms, has opened up an alternative way of production. Chaetoceros gracilis is one of the diatoms, which is potential in producing silaffin protein. This study aimed to isolate and to characterize the protein. We also analyzed the protein activity toward tetraethoxyorthosilicate (TEOS substrate in in vitro reaction. Diatom biomass was harvested and further kept in 2% SDS/100 mM EDTA solution. Protein isolation was conducted by dissolving the silica and separating the protein by soaking in 2 M HF/8 M NH4F. Protein concentration was analyzed using Bradford method and the molecular weight was estimated through SDS-PAGE. Protein activity was observed by reacting it with TEOS substrate to form silica polymer and measured by colorimetric molibdate assay. Protein concentration was 1.20 mg/ml and appeared filamentous. The apparent molecular weights consisted of 12, 23, 42, 44 kDa. These protein was able to polymerize the silica at room temperature within 10 min. As much as 85.65 mol TEOS was polymerized per 1.4 x 106 silaffin protein per min. SEM analysis showed the formation of spherical, aggregate biosilica.

Deposition of molecular probes in heavy ion tracks

CERN Document Server

Esser, M

1999-01-01

By using polarized fluorescence techniques the physical properties of heavy ion tracks such as the dielectric number, molecular alignment and track radius can be traced by molecular fluorescence probes. Foils of poly(ethylene terephthalate) (PET) were used as a matrix for the ion tracks wherein fluorescence probes such as aminostyryl-derivatives can be incorporated using a suitable solvent, e.g. N,N'-dimethylformamide (DMF) as transport medium. The high sensitivity of fluorescence methods allowed the comparison of the probe properties in ion tracks with the virgin material. From the fluorescence Stokes shift the dielectric constants could be calculated, describing the dielectric surroundings of the molecular probes. The lower dielectric constant in the tracks gives clear evidence that there is no higher accommodation of the highly polar solvent DMF in the tracks compared with the virgin material. Otherwise the dielectric constant in the tracks should be higher than in the virgin material. The orientation of t...

Sampler collection gadget for epilithic diatoms

Directory of Open Access Journals (Sweden)

SE. Salomoni

Full Text Available This work present a new gadget for sampling epilithic diatoms from both lentic and lotic enviroments. The sampler consists of a polystyrene cylinder, left to float on the surface of the water, to which stone substrates are attached. This epilithic diatom sampler (EDS can be used to detect spatial and temporal richness and density variation in the study of the diatom community, as well as in water quality monitoring.

Low pressure gas detectors for molecular-ion break up studies

International Nuclear Information System (INIS)

Breskin, A.; Chechik, R.; Zwang, N.

1981-01-01

Two detector systems for Molecular ions like OH + and CH 2 + and like H 2 + and H 3 + were developed and are described. The first detector is installed in a magnetic spectrometer. Both systems are made of various types of gas detectors operating at low pressures. In the study of the Coulomb explosion of molecular ions like OH + , CH 2 + or H 3 + these detectors provide the position and time coordinates of all the fragments of the molecular ion, in coincidence, in order to determine their energy and angular distribution. In the case of molecules containing atoms other than hydrogen, information on the electronic charge state is obtained. (H.K.)

Colloquium on diatom-copepod interactions

DEFF Research Database (Denmark)

Paffenhofer, G.A.; Ianora, A.; Miralto, A.

2005-01-01

in situ were also addressed. During the plenary session, the most recent advances on this topic were presented. The plenary session was followed by 3 working groups on (1) production of aldehydes by phytoplankton, (2) toxic and nutritional effects of diatoms on zooplankton, and (3) the chemistry of diatom...

Molecular and Photosynthetic Responses to Prolonged Darkness and Subsequent Acclimation to Re-Illumination in the Diatom Phaeodactylum tricornutum

DEFF Research Database (Denmark)

Nymark, Marianne; Valle, Kristi Collier; Hancke, Kasper

2013-01-01

and immediately utilize the available energy in photosynthesis and growth. We have investigated both the response to prolonged darkness and the re-acclimation to moderate intensity white irradiance (E = 100 µmol m−2 s−1) in the diatom Phaeodactylum tricornutum, using an integrated approach involving global......-introduction of the cells to the initial light conditions revealed 5) distinct expression profiles for nuclear genes involved in photosynthesis and those involved in photoprotection, 6) rapid rise in photosynthetic parameters (α and rETRmax) within 0.5 h of re-exposure to light despite a very modest de novo synthesis......Photosynthetic diatoms that live suspended throughout the water column will constantly be swept up and down by vertical mixing. When returned to the photic zone after experiencing longer periods in darkness, mechanisms exist that enable the diatoms both to survive sudden light exposure...

The role of ro-vibrational coupling in the revival dynamics of diatomic molecular wave packets

International Nuclear Information System (INIS)

Banerji, J; Ghosh, Suranjana

2006-01-01

We study the revival and fractional revivals of a diatomic molecular wave packet of circular states whose weighing coefficients are peaked about a vibrational quantum number ν-bar and a rotational quantum number j-bar. Furthermore, we show that the interplay between the rotational and vibrational motion is determined by a parameter γ =√D/C, where D is the dissociation energy and C is inversely proportional to the reduced mass of the two nuclei. Using I 2 and H 2 as examples, we show, both analytically and visually (through animations), that for γ>>ν-bar, j-bar, the rotational and vibrational time scales are so far apart that the ro-vibrational motion gets decoupled and the revival dynamics depends essentially on one time scale. For γ∼ν-bar, j-bar, on the other hand, the evolution of the wave packet depends crucially on both the rotational and vibrational time scales of revival. In the latter case, an interesting rotational-vibrational fractional revival is predicted and explained

Variation partitioning of diatom species data matrices: Understanding the influence of multiple factors on benthic diatom communities in tropical streams

Energy Technology Data Exchange (ETDEWEB)

Bere, Taurai, E-mail: tbere2015@gmail.com; Mangadze, Tinotenda; Mwedzi, Tongai

2016-10-01

Elucidating the confounding influence of multiple environmental factors on benthic diatom communities is important in developing water quality predictive models for better guidance of stream management efforts. The objective of this study was to explore the relative impact of metal pollution and hydromorphological alterations in, addition to nutrient enrichment and organic pollution, on diatom taxonomic composition with the view to improve stream diatom-based water quality inference models. Samples were collected twice at 20 sampling stations in the tropical Manyame Catchment, Zimbabwe. Diatom, macroinvertebrate communities and environmental factors were sampled and analysed. The variations in diatom community composition explained by different categories of environmental factors were analysed using canonical correspondence analysis using variance partitioning (partial CCA). The following variations were explained by the different predictor matrices: nutrient levels and organic pollution - 10.4%, metal pollution - 8.3% and hydromorphological factors - 7.9%. Thus, factors other than nutrient levels and organic pollution explain additional significant variation in these diatom communities. Development of diatom-based stream water quality inference models that incorporate metal pollution and hydromorphological alterations, where these are key issues, is thus deemed necessary. - Highlights: • Confounding influences of multiple environmental factors on diatom communities are elucidated. • Variation explained: nutrients + organic pollution - 10.4%, metals - 8.3% and hydromorphological factors - 7.9%. • Calibration of existing or development of new indices may be necessary.

Variation partitioning of diatom species data matrices: Understanding the influence of multiple factors on benthic diatom communities in tropical streams

International Nuclear Information System (INIS)

Bere, Taurai; Mangadze, Tinotenda; Mwedzi, Tongai

2016-01-01

Elucidating the confounding influence of multiple environmental factors on benthic diatom communities is important in developing water quality predictive models for better guidance of stream management efforts. The objective of this study was to explore the relative impact of metal pollution and hydromorphological alterations in, addition to nutrient enrichment and organic pollution, on diatom taxonomic composition with the view to improve stream diatom-based water quality inference models. Samples were collected twice at 20 sampling stations in the tropical Manyame Catchment, Zimbabwe. Diatom, macroinvertebrate communities and environmental factors were sampled and analysed. The variations in diatom community composition explained by different categories of environmental factors were analysed using canonical correspondence analysis using variance partitioning (partial CCA). The following variations were explained by the different predictor matrices: nutrient levels and organic pollution - 10.4%, metal pollution - 8.3% and hydromorphological factors - 7.9%. Thus, factors other than nutrient levels and organic pollution explain additional significant variation in these diatom communities. Development of diatom-based stream water quality inference models that incorporate metal pollution and hydromorphological alterations, where these are key issues, is thus deemed necessary. - Highlights: • Confounding influences of multiple environmental factors on diatom communities are elucidated. • Variation explained: nutrients + organic pollution - 10.4%, metals - 8.3% and hydromorphological factors - 7.9%. • Calibration of existing or development of new indices may be necessary.

Cadmium sensitivity, uptake, subcellular distribution and thiol induction in a marine diatom: Exposure to cadmium

International Nuclear Information System (INIS)

Wang Mengjiao; Wang Wenxiong

2011-01-01

The aims of this study were to (1) evaluate the changes in the Cd tolerance of a marine diatom after exposure under different Cd concentrations for various durations and (2) to explore the potential subcellular and biochemical mechanisms underlying these changes. The 72-h toxicity, short-term Cd uptake, subcellular Cd distribution, as well as the synthesis of phytochelatins (PCs) were measured in a marine diatom Thalassiosira nordenskioeldii after exposure to a range of free Cd ion concentrations ([Cd 2+ ], 0.01-84 nM) for 1-15 days. Surprisingly, the diatoms did not acquire higher resistance to Cd after exposure; instead their sensitivity to Cd increased with a higher exposed [Cd 2+ ] and a longer exposure period. The underlying mechanisms could be traced to the responses of Cd cellular accumulation and the intrinsic detoxification ability of the preconditioned diatoms. Generally, exposure to a higher [Cd 2+ ] and for a longer period increased the Cd uptake rate, cellular accumulation, as well as the Cd concentration in metal-sensitive fraction (MSF) in these diatoms. In contrast, although PCs were induced by the environmental Cd stress (with PC 2 being the most affected), the increased intracellular Cd to PC-SH ratio implied that the PCs' detoxification ability had reduced after Cd exposure. All these responses resulted in an elevated Cd sensitivity as exposed [Cd 2+ ] and duration increased. This study shows that the physiological/biochemical and kinetic responses of phytoplankton upon metal exposure deserve further investigation.

A molecular beam machine for the measurement of the scattering of polar diatomic molecules

International Nuclear Information System (INIS)

Everdij, J.J.

1976-01-01

This thesis describes an experimental method to determine the long range, angular dependent part of the intermolecular potential between a polar diatomic molecule and a spherical symmetric partner. The method contains the study of the scattering behaviour of the molecules in a crossed beam experiment. The primary beam consisting of polar diatomic molecules at thermal velocities (approximately 0.1 eV), is selected in a specified rotational state by means of an electrostatic, inhomogeneous field before the scattering center, where it crosses the (supersonic) secondary beam under an angle of 90 0 . By means of a second state selector, followed by a velocity selector and a particle detector, the consequences are studied of the scattering process on the primary beam, i.e. the behaviour of the total and differential elastic cross sections plus the transition probability of a collision induced transition to another rotational state. (Auth.)

Physics with colder molecular ions: The Heidelberg Cryogenic Storage Ring CSR

International Nuclear Information System (INIS)

Zajfman, D; Wolf, A; Schwalm, D; Orlov, D A; Grieser, M; Hahn, R von; Welsch, C P; Lopez-Urrutia, J R Crespo; Schroeter, C D; Urbain, X; Ullrich, J

2005-01-01

A novel cryogenic electrostatic storage ring is planned to be built at the Max-Planck Institute for Nuclear Physics in Heidelberg. The machine is expected to operate at low temperatures (∼2K) and to store beams with kinetic energies between 20 to 300 keV. An electron target based on cooled photocathode technology will serve as a major tool for the study of reactions between molecular ions and electrons. Moreover, atomic beams can be merged and crossed with the stored ion beams allowing for atom molecular-ion collision studies at very low up to high relative energies. The proposed experimental program, centered around the physics of cold molecular ions, is shortly outlined

Periodic orbits of the hydrogen molecular ion and their quantization

International Nuclear Information System (INIS)

Duan, Y.; Yuan, J.; Bao, C.

1995-01-01

In a classical study of the hydrogen molecular ion beyond the Born-Oppenheimer approximation (BOA), we have found that segments of trajectories resemble that of the Born-Oppenheimer approximation periodic orbits. The importance of this fact to the classical understanding of chemical bonding leads us to a systematic study of the periodic orbits of the planar hydrogen molecular ion within the BOA. Besides introducing a classification scheme for periodic orbits, we discuss the convergence properties of families of periodic orbits and their bifurcation patterns according to their types. Semiclassical calculations of the density of states based on these periodic orbits yield results in agreement with the exact quantum eigenvalues of the hydrogen molecular ion system

Collision induced fragmentation of fast molecular ions in solids and gases

International Nuclear Information System (INIS)

Gemmell, D.S.

1979-01-01

A brief review is given of recent high resolution measurements on fragments arising from the collision-induced dissociation of fast (MeV) molecular ions. For solid targets, strong wake effects are observed. For gaseous targets, excited electronic states of the projectile ions play an important role. Measurements of this type provide useful information on the charge states of fast ions traversing matter. The experimental techniques show promise as a unique method for determining the geometrical structures of the molecular-ion projectiles. 41 references

Diatom genomics: genetic acquisitions and mergers.

Science.gov (United States)

Nisbet, R Ellen R; Kilian, Oliver; McFadden, Geoffrey I

2004-12-29

Diatom algae arose by two-step endosymbiosis. The complete genome of the diatom Thalassiosira pseudonana has now been sequenced, allowing us to reconstruct the remarkable intracellular gene transfers that occurred during this convoluted cellular evolution.

Towards an understanding of the molecular regulation of carbon allocation in diatoms: the interaction of energy and carbon allocation.

Science.gov (United States)

Wagner, Heiko; Jakob, Torsten; Fanesi, Andrea; Wilhelm, Christian

2017-09-05

In microalgae, the photosynthesis-driven CO 2 assimilation delivers cell building blocks that are used in different biosynthetic pathways. Little is known about how the cell regulates the subsequent carbon allocation to, for example, cell growth or for storage. However, knowledge about these regulatory mechanisms is of high biotechnological and ecological importance. In diatoms, the situation becomes even more complex because, as a consequence of their secondary endosymbiotic origin, the compartmentation of the pathways for the primary metabolic routes is different from green algae. Therefore, the mechanisms to manipulate the carbon allocation pattern cannot be adopted from the green lineage. This review describes the general pathways of cellular energy distribution from light absorption towards the final allocation of carbon into macromolecules and summarizes the current knowledge of diatom-specific allocation patterns. We further describe the (limited) knowledge of regulatory mechanisms of carbon partitioning between lipids, carbohydrates and proteins in diatoms. We present solutions to overcome the problems that hinder the identification of regulatory elements of carbon metabolism.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Author(s).

Metal ion sequestration: An exciting dimension for molecularly ...

African Journals Online (AJOL)

The use of a tight binding macrocyclic ligand to complex a metal ion so that this serves as receptee on the Molecularly Imprinted Polymer (MIP) receptor as described here affords a sequestration route for a targeted metal ion, with potential for environmental remediation and restoration applications. Ethylene glycol ...

Coupled states approximation for scattering of two diatoms

International Nuclear Information System (INIS)

Heil, T.G.; Green, S.; Kouri, D.J.

1978-01-01

The coupled states (CS) approximation is developed in detail for the general case of two colliding diatomic molecules. The high energy limit of the exact Lippmann-Schwinger equation is used to obtain the CS equations so that the sufficiency conditions of Kouri, Heil, and Shimoni apply. In addition, care is taken to ensure correct treatment of parity in the CS, as well as correct labeling of the CS by an effective orbital angular momentum. The analysis follows that given by Shimoni and Kouri for atom-diatom collisions where the coupled rotor angular momentum j 12 and projection lambda 12 replace the single diatom angular momentum j and projection lambda. The result is an expression for the differential scattering amplitude which is a generalization of the highly successful McGuire-Kouri differential scattering amplitude for atom-diatom collisions. Also, the opacity function is found to be a generalization of the Clebsch-Gordon weight atom-diatom expression of Shimoni and Kouri. The diatom-diatom CS body frame T matrix T/sup J/(j 1 'j 2 'j 12 'lambda 12 'vertical-bar j 1 j 2 j 12 lambda 12 ) is also found to be nondiagonal in lambda' 12 ,lambda 12 , just as in the atom-diatom case. The parity and identical molecule interchange symmetries are also considered in detail in both the exact close coupling and CS approximations. Symmetrized expressions for all relevant quantities are obtained, along with the symmetrized coupled equations one must solve. The properly labeled and symmetrized CS equations have not been derived before this present work. The present correctly labeled CS theory is tested computationally by applications to three different diatom-diatom potentials. First we carry out calculations for para-para, ortho-ortho, and ortho-para H 2 -H 2 collisions using the experimental potential of Farrar and Lee

Approximate Solutions of Schrodinger Equation with Some Diatomic Molecular Interactions Using Nikiforov-Uvarov Method

Directory of Open Access Journals (Sweden)

Ituen B. Okon

2017-01-01

Full Text Available We used a tool of conventional Nikiforov-Uvarov method to determine bound state solutions of Schrodinger equation with quantum interaction potential called Hulthen-Yukawa inversely quadratic potential (HYIQP. We obtained the energy eigenvalues and the total normalized wave function. We employed Hellmann-Feynman Theorem (HFT to compute expectation values r-2, r-1, T, and p2 for four different diatomic molecules: hydrogen molecule (H2, lithium hydride molecule (LiH, hydrogen chloride molecule (HCl, and carbon (II oxide molecule. The resulting energy equation reduces to three well-known potentials which are as follows: Hulthen potential, Yukawa potential, and inversely quadratic potential. The bound state energies for Hulthen and Yukawa potentials agree with the result reported in existing literature. We obtained the numerical bound state energies of the expectation values by implementing MATLAB algorithm using experimentally determined spectroscopic constant for the different diatomic molecules. We developed mathematica programming to obtain wave function and probability density plots for different orbital angular quantum number.

Guiding of slow neon and molecular hydrogen ions through nanocapillaries in PET

International Nuclear Information System (INIS)

Stolterfoht, N.; Hellhammer, R.; Sobocinski, P.; Pesic, Z.D.; Bundesmann, J.; Sulik, B.; Shah, M.B.; Dunn, K.; Pedregosa, J.; McCullough, R.W.

2005-01-01

The transmission profiles of atomic 3keV Ne 7+ ions and molecular 1keV H 2 + and H 3 + ions passing through nanocapillaries were studied. Capillaries with a diameter of 100nm and a length of 10μm in insulating PET polymers were used. The high aspect ratio of 100 is achieved by the method of etching ion tracks produced by high-energy xenon impact. The angular distributions of the transmitted projectiles show that the majority of ions are transported in their initial charge state along the capillary axis even when the capillaries are tilted with respect to the incident beam direction. This result indicates ion-guiding, which is produced by charge-up effects influencing the ion trajectories in a self-supporting manner. The guiding effects are found to be different for highly charged neon and singly charged molecular hydrogen. Negligible fragmentation of the molecular ions was observed

Relaxed geometries and dipole moments of positron complexes with diatomic molecules

Energy Technology Data Exchange (ETDEWEB)

Assafrao, Denise; Mohallem, Jose R, E-mail: rachid@fisica.ufmg.b [Laboratorio de Atomos e Moleculas Especiais, Departamento de Fisica, ICEx, Universidade Federal de Minas Gerais, CP 702, 30123-970, Belo Horizonte, MG (Brazil)

2010-01-01

Relaxed geometries and dipole moments of diatomic molecules interacting with a slow positron are reported as functions of the positron distance to the more electronegative atom. A molecular model for the complex that allows applications to large systems is used. The electron population on the positron is proposed as a weighting function to calculate the average quantities. Results show Self-Consistent-Field quality or better.

Applications of Diatoms as Potential Microalgae in Nanobiotechnology

Directory of Open Access Journals (Sweden)

Ahmad Yari Khosroushahi

2012-05-01

Full Text Available Introduction: Diatoms are single cell eukaryotic microalgae, which present in nearly every water habitat make them ideal tools for a wide range of applications such as oil explora­tion, forensic examination, environmental indication, biosilica pattern generation, toxicity testing and eutrophication of aqueous ecosystems. Methods: Essential information on diatoms were reviewed and discussed towards impacts of diatoms on biosynthesis and bioremediation. Results: In this review, we present the recent progress in this century on the application of diatoms in waste degradation, synthesis of biomaterial, biomineraliza­tion, toxicity and toxic effects of mineral elements evaluations. Conclusion: Diatoms can be considered as metal toxicity bioindicators and they can be applied for biomineralization, synthesis of biomaterials, and degradation of wastes.

Structure-based optics of centric diatom frustules: modulation of the in vivo light field for efficient diatom photosynthesis.

Science.gov (United States)

Goessling, Johannes W; Su, Yanyan; Cartaxana, Paulo; Maibohm, Christian; Rickelt, Lars F; Trampe, Erik C L; Walby, Sandra L; Wangpraseurt, Daniel; Wu, Xia; Ellegaard, Marianne; Kühl, Michael

2018-07-01

The optical properties of diatom silicate frustules inspire photonics and nanotechnology research. Whether light interaction with the nano-structure of the frustule also affects diatom photosynthesis has remained unclear due to lack of information on frustule optical properties under more natural conditions. Here we demonstrate that the optical properties of the frustule valves in water affect light harvesting and photosynthesis in live cells of centric diatoms (Coscinodiscus granii). Microscale cellular mapping of photosynthesis around localized spot illumination demonstrated optical coupling of chloroplasts to the valve wall. Photonic structures of the three-layered C. granii valve facilitated light redistribution and efficient photosynthesis in cell regions distant from the directly illuminated area. The different porous structure of the two sides of the valve exhibited photon trapping and forward scattering of blue light enhancing photosynthetic active radiation inside the cell. Photonic structures of diatom frustules thus alter the cellular light field with implications on diatom photobiology. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Diatom community structure on in-service cruise ship hulls.

Science.gov (United States)

Hunsucker, Kelli Zargiel; Koka, Abhishek; Lund, Geir; Swain, Geoffrey

2014-10-01

Diatoms are an important component of marine biofilms found on ship hulls. However, there are only a few published studies that describe the presence and abundance of diatoms on ships, and none that relate to modern ship hull coatings. This study investigated the diatom community structure on two in-service cruise ships with the same cruise cycles, one coated with an antifouling (AF) system (copper self-polishing copolymer) and the other coated with a silicone fouling-release (FR) system. Biofilm samples were collected during dry docking from representative areas of the ship and these provided information on the horizontal and vertical zonation of the hull, and intact and damaged coating and niche areas. Diatoms from the genera Achnanthes, Amphora and Navicula were the most common, regardless of horizontal ship zonation and coating type. Other genera were abundant, but their presence was more dependent on the ship zonation and coating type. Samples collected from damaged areas of the hull coating had a similar community composition to undamaged areas, but with higher diatom abundance. Diatom fouling on the niche areas differed from that of the surrounding ship hull and paralleled previous studies that investigated differences in diatom community structure on static and dynamically exposed coatings; niche areas were similar to static immersion and the hull to dynamic immersion. Additionally, diatom richness was greater on the ship with the FR coating, including the identification of several new genera to the biofouling literature, viz. Lampriscus and Thalassiophysa. These results are the first to describe diatom community composition on in-service ship hulls coated with a FR system. This class of coatings appears to have a larger diatom community compared to copper-based AF systems, with new diatom genera that have the ability to stick to ship hulls and withstand hydrodynamic forces, thus creating the potential for new problematic species in the biofilm.

Mean excitation energies for molecular ions

DEFF Research Database (Denmark)

Jensen, Phillip W.K.; Sauer, Stephan P.A.; Oddershede, Jens

2017-01-01

The essential material constant that determines the bulk of the stopping power of high energy projectiles, the mean excitation energy, is calculated for a range of smaller molecular ions using the RPA method. It is demonstrated that the mean excitation energy of both molecules and atoms increase...

Electrophoretic protein profiles of mid-sized copepod Calanoides patagoniensis steadily fed bloom-forming diatoms

Directory of Open Access Journals (Sweden)

Victor M Aguilera

2015-09-01

Full Text Available Recent field and experimental evidence collected in the southern upwelling region off Concepción (36°5'S, 73°3'W showed an abrupt reduction (<72 h in the egg production rates (EPR of copepods when they were fed steadily and solely with the local bloom-forming diatom Thalassiosira rotula. Because diatoms were biochemically similar to dinoflagellate Prorocentrum minimum, a diet which supported higher reproductive outcomes, the fecundity reduction observed in copepod females fed with the diatom may have obeyed to post-ingestive processes, giving rise to resources reallocation. This hypothesis was tested by comparing feeding (clearance and ingestion rates, reproduction (EPR and hatching success and the structure of protein profiles (i.e., number and intensity of electrophoretic bands of copepods (adults and eggs incubated during 96 h with the two food conditions. The structure of protein profiles included molecular sizes that were calculated from the relative mobility of protein standards against the logarithm of their molecular sizes. After assessing the experimental conditions, feeding decreased over time for those females fed with T. rotula, while reproduction was higher in females fed with P. minimum. Electrophoretic profiles resulted similar mostly at a banding region of 100 to 89-kDa, while they showed partial differences around the region of 56-kDa band, especially in those females fed and eggs produced with T. rotula. Due to reproductive volume was impacted while larvae viability, a physiological processes with specific and high nutritional requirements, was independent on food type; post-ingestive processes, such as expression of stress-related proteins deviating resources to metabolic processes others than reproduction, are discussed under framework of nutritional-toxic mechanisms mediating copepod-diatoms relationships in productive upwelling areas.

Relationship between diatom communities and environmental ...

African Journals Online (AJOL)

ajl yemi

2011-11-30

Nov 30, 2011 ... The relationship between diatom species and measured environmental variables was explored at different sites of Honghe wetland region located in northeastern China. Planktonic and epiphytic diatom assemblages in the wetland were identified from May to October of 2007 and 2008. Their relationships.

Relationship between diatom communities and environmental ...

African Journals Online (AJOL)

Abstract. The relationship between diatom species and measured environmental variables was explored at different sites of Honghe wetland region located in northeastern China. Planktonic and epiphytic diatom assemblages in the wetland were identified from May to October of 2007 and 2008. Their relationships with ...

Selective silicate-directed motility in diatoms

DEFF Research Database (Denmark)

Bondoc, Karen Grace V.; Heuschele, Jan; Gillard, Jeroen

2016-01-01

the major sink in the global Si cycle. Dissolved silicic acid (dSi) availability frequently limits diatom productivity and influences species composition of communities. We show that benthic diatoms selectively perceive and behaviourally react to gradients of dSi. Cell speed increases under d...

Determination of molecular-ion structures through the use of accelerated beams

International Nuclear Information System (INIS)

Gemmell, D.S.

1987-01-01

In this talk we report on recent research on molecular-ion structures using fast molecular-ion beams provided by Argonne's 5-MV Dynamitron accelerator. The method has become known as the ''Coulomb-explosion'' technique. When molecular-ion projectiles travelling at velocities of a few percent of the velocity of light strike a foil, the electrons that bind the molecular projectiles are almost always totally stripped off within the first few Angstroms of penetration into the solid target. This leaves a cluster of bare (or nearly bare) nuclei which separate rapidly as a result of their mutual Coulomb repulsion. This violent dissociation process in which the initial electrostatic potential energy is converted into kinetic energy of relative motion in the center-of-mass, has been termed a ''Coulomb explosion.'' 4 refs., 2 figs

Formation and fragmentation of quadruply charged molecular ions by intense femtosecond laser pulses.

Science.gov (United States)

Yatsuhashi, Tomoyuki; Nakashima, Nobuaki

2010-07-22

We investigated the formation and fragmentation of multiply charged molecular ions of several aromatic molecules by intense nonresonant femtosecond laser pulses of 1.4 mum with a 130 fs pulse duration (up to 2 x 10(14) W cm(-2)). Quadruply charged states were produced for 2,3-benzofluorene and triphenylene molecular ion in large abundance, whereas naphthalene and 1,1'-binaphthyl resulted only in up to triply charged molecular ions. The laser wavelength was nonresonant with regard to the electronic transitions of the neutral molecules, and the degree of fragmentation was strongly correlated with the absorption of the singly charged cation radical. Little fragmentation was observed for naphthalene (off-resonant with cation), whereas heavy fragmentation was observed in the case of 1,1'-binaphthyl (resonant with cation). The degree of H(2) (2H) and 2H(2) (4H) elimination from molecular ions increased as the charge states increased in all the molecules examined. A striking difference was found between triply and quadruply charged 2,3-benzofluorene: significant suppression of molecular ions with loss of odd number of hydrogen was observed in the quadruply charged ions. The Coulomb explosion of protons in the quadruply charged state and succeeding fragmentation resulted in the formation of triply charged molecular ions with an odd number of hydrogens. The hydrogen elimination mechanism in the highly charged state is discussed.

Electron impact study of molecular ions of some benzyl derivatives

International Nuclear Information System (INIS)

Selim, E.T.; Rabia, M.A.; Fahmy, M.A.

1992-01-01

The ionization energies at threshold and values of higher energy levels for the molecular ions of benzyl alcohol, benzyl amine and benzyl cyanide are reported using electron impact technique. The first ionization energy values are found to be 8.26 eV (benzyl alcohol), 8.49 eV(benzyl amine)and 9.32 eV (benzyl cyanide). Some of the reported higher energy levels for the molecular ions are tentatively explained. The differences in the relative abundances for the main fragment ions are discussed and attributed to the effect of the different substituents - OH, -NH2 and -CN groups

The transcription factor bZIP14 regulates the TCA cycle in the diatom Phaeodactylum tricornutum.

Science.gov (United States)

Matthijs, Michiel; Fabris, Michele; Obata, Toshihiro; Foubert, Imogen; Franco-Zorrilla, José Manuel; Solano, Roberto; Fernie, Alisdair R; Vyverman, Wim; Goossens, Alain

2017-06-01

Diatoms are amongst the most important marine microalgae in terms of biomass, but little is known concerning the molecular mechanisms that regulate their versatile metabolism. Here, the pennate diatom Phaeodactylum tricornutum was studied at the metabolite and transcriptome level during nitrogen starvation and following imposition of three other stresses that impede growth. The coordinated upregulation of the tricarboxylic acid (TCA) cycle during the nitrogen stress response was the most striking observation. Through co-expression analysis and DNA binding assays, the transcription factor bZIP14 was identified as a regulator of the TCA cycle, also beyond the nitrogen starvation response, namely in diurnal regulation. Accordingly, metabolic and transcriptional shifts were observed upon overexpression of bZIP14 in transformed P. tricornutum cells. Our data indicate that the TCA cycle is a tightly regulated and important hub for carbon reallocation in the diatom cell during nutrient starvation and that bZIP14 is a conserved regulator of this cycle. © 2017 The Authors.

9 Records of Diatoms and Physicochemical.cdr

African Journals Online (AJOL)

Administrator

between some physicochemical parameters and diatom species in these ponds. ..... Diversity and relative abundance (%) of diatoms species in selected seasonal ponds in Zaria, Nigeria ..... connection with reference conditions of the water.

Molecular physics. Theoretical principles and experimental methods

International Nuclear Information System (INIS)

Demtroeder, W.

2005-01-01

This advanced textbook comprehensively explains important principles of diatomic and polyatomic molecules and their spectra in two separate, distinct parts. The first part concentrates on the theoretical aspects of molecular physics, whereas the second part of the book covers experimental techniques, i.e. laser, Fourier, NMR, and ESR spectroscopies, used in the fields of physics, chemistry, biolog, and material science. Appropriate for undergraduate and graduate students in physics and chemistry with a knowledge of atomic physics and familiar with the basics of quantum mechanics. From the contents: - Electronic States of Molecules, - Rotation, Oscillation and Potential Curves of Diatomic Molecules, - The Spectra of Diatomic Molecules, - Molecule Symmetries and Group Theory, - Rotation and Oscillations of Polyatomic Molecules, - Electronic States of Polyatomic Molecules, - The Spectra of Polyatomic Molecules, - Collapse of the Born-Oppenheimer-Approximation, Disturbances in Molecular Spectra, - Molecules in Disturbing Fields, - Van-der-Waals-Molecules and Cluster, - Experimental Techniques in Molecular Physics. (orig.)

Method for preparation and readout of polyatomic molecules in single quantum states

Science.gov (United States)

Patterson, David

2018-03-01

Polyatomic molecular ions contain many desirable attributes of a useful quantum system, including rich internal degrees of freedom and highly controllable coupling to the environment. To date, the vast majority of state-specific experimental work on molecular ions has concentrated on diatomic species. The ability to prepare and read out polyatomic molecules in single quantum states would enable diverse experimental avenues not available with diatomics, including new applications in precision measurement, sensitive chemical and chiral analysis at the single-molecule level, and precise studies of Hz-level molecular tunneling dynamics. While cooling the motional state of a polyatomic ion via sympathetic cooling with a laser-cooled atomic ion is straightforward, coupling this motional state to the internal state of the molecule has proven challenging. Here we propose a method for readout and projective measurement of the internal state of a trapped polyatomic ion. The method exploits the rich manifold of technically accessible rotational states in the molecule to realize robust state preparation and readout with far less stringent engineering than quantum logic methods recently demonstrated on diatomic molecules. The method can be applied to any reasonably small (≲10 atoms) polyatomic ion with an anisotropic polarizability.

Modeling ion sensing in molecular electronics

International Nuclear Information System (INIS)

Chen, Caroline J.; Smeu, Manuel; Ratner, Mark A.

2014-01-01

We examine the ability of molecules to sense ions by measuring the change in molecular conductance in the presence of such charged species. The detection of protons (H + ), alkali metal cations (M + ), calcium ions (Ca 2+ ), and hydronium ions (H 3 O + ) is considered. Density functional theory (DFT) is used within the Keldysh non-equilibrium Green's function framework (NEGF) to model electron transport properties of quinolinedithiol (QDT, C 9 H 7 NS 2 ), bridging Al electrodes. The geometry of the transport region is relaxed with DFT. The transport properties of the device are modeled with NEGF-DFT to determine if this device can distinguish among the M + + QDT species containing monovalent cations, where M + = H + , Li + , Na + , or K + . Because of the asymmetry of QDT in between the two electrodes, both positive and negative biases are considered. The electron transmission function and conductance properties are simulated for electrode biases in the range from −0.5 V to 0.5 V at increments of 0.1 V. Scattering state analysis is used to determine the molecular orbitals that are the main contributors to the peaks in the transmission function near the Fermi level of the electrodes, and current-voltage relationships are obtained. The results show that QDT can be used as a proton detector by measuring transport through it and can conceivably act as a pH sensor in solutions. In addition, QDT may be able to distinguish among different monovalent species. This work suggests an approach to design modern molecular electronic conductance sensors with high sensitivity and specificity using well-established quantum chemistry

Molecular effects in ion-electron emission from clean metal surfaces

International Nuclear Information System (INIS)

Baragiola, R.A.; Alonso, E.V.; Auciello, O.; Ferron, J.; Lantschner, G.; Oliva Florio, A.

1978-01-01

The authors have measured electron emission yields from clean Al, Cu and Ag under 2-50 keV H + , D + , H 2 + impact. It is found that molecular ion yields are lower than twice the yield of atomic ions. No isotope effects are observed for equal-velocity ions. (Auth.)

Ion-molecular equilibria and activity determination in the RbF-ZrF4 system

International Nuclear Information System (INIS)

Skokan, E.V.; Nikitin, M.I.; Sorokin, I.D.; Korenev, Yu.M.; Sidorov, L.N.

1983-01-01

Activity of zirconium tetrofluoride in 100-33.3 mol % ZrF 4 concentration range was determined during isothermal evaporation of samples of different initial composition of RbF-ZrF 4 system, using ion-molecular equilibrium method. It became possible, using the exchange ion-molecular reactions to determine ZrF 4 activity approximately 10 -10 in the region of state diagram of RbF-ZrF 4 system, adjoining to rubidium fluoride. The comparative analysis of results, obtained by the methods of isothermal evaporation, ion-molecular equilibria is given; the advantages and restrictions of ion-molecular equilibrium method are presented

Potential of diatom consortium developed by nutrient enrichment for biodiesel production and simultaneous nutrient removal from waste water

Directory of Open Access Journals (Sweden)

Thomas Kiran Marella

2018-05-01

Full Text Available Because of the decreasing fossil fuel supply and increasing greenhouse gas (GHG emissions, microalgae have been identified as a viable and sustainable feedstock for biofuel production. The major effect of the release of wastewater rich in organic compounds has led to the eutrophication of freshwater ecosystems. A combined approach of freshwater diatom cultivation with urban sewage water treatment is a promising solution for nutrient removal and biofuel production. In this study, urban wastewater from eutrophic Hussain Sagar Lake was used to cultivate a diatom algae consortium, and the effects of silica and trace metal enrichment on growth, nutrient removal, and lipid production were evaluated. The nano-silica-based micronutrient mixture Nualgi containing Si, Fe, and metal ions was used to optimize diatom growth. Respectively, N and P reductions of 95.1% and 88.9%, COD and BOD reductions of 91% and 51% with a biomass yield of 122.5 mg L−1 day−1 and lipid productivity of 37 mg L−1 day−1 were observed for cultures grown in waste water using Nualgi. Fatty acid profiles revealed 13 different fatty acids with slight differences in their percentage of dry cell weight (DCW depending on enrichment level. These results demonstrate the potential of diatom algae grown in wastewater to produce feedstock for renewable biodiesel production. Enhanced carbon and excess nutrient utilization makes diatoms ideal candidates for co-processes such as CO2 sequestration, biodiesel production, and wastewater phycoremediation. Keywords: Micro algae, Diatom, Biodiesel, Nualgi, Nutrient removal, Wastewater

Ion-molecular reactions initiated by β-decay of tritium in tritiated compounds

International Nuclear Information System (INIS)

Akulov, G.P.

1976-01-01

Ion-molecular reactions initiated by β-decay of tritium and tritiated hydrocarbons have been systematized. The review describes the theoretical and experimental foundation of the radiochemical method of this important type of chemical interactions investigation. The reactions of the molecular ions of HeT + with methane, ethane, propane, butane and also with cycloalkanes from C 3 to C 6 are discussed. The reactions under consideration have been united into two groups: reactions involving HeT + ions and those involving carbonic ions. From the experimental results available, the conclusions have been drawn about the reactivity of these intermediate formations, about the mechanism of their interaction with organic substances, and also about the perspectives of using the radiochemical method in studies of ion-molecular reactions. The experimental results published before May 1974 are examined. The bibliography includes 162 references

Photodissociation from a manifold of rovibrational states and free-free absorption by a diatomic molecule

International Nuclear Information System (INIS)

Lebedev, V S; Presnyakov, L P

2002-01-01

An analytical approach for the description of photoabsorption by a gas or plasma medium containing atomic and molecular components in thermodynamic equilibrium is developed. Continuous absorption of radiation is due to the photodissociation of a diatomic molecule from a manifold of excited rovibrational states and free-free transitions between the two electronic terms of a quasimolecule temporarily formed during a collision of atomic particles. The formulae are obtained for individual photodissociation cross sections from a given rovibrational state and for the Boltzmann-averaged cross section. Particular attention is paid to the derivation of a general analytical expression for the total absorption coefficient including the integral contribution of bound-free and free-free radiative transitions. The consideration is based on the theory of nonadiabatic transitions combined with the approximation of a quasicontinuum for rovibrational states. The theory is applied to the investigation of photoabsorption by the H 2 + ion in the IR, visible and UV spectral regions. It is shown that our results are in good agreement with available ab initio quantal calculations of photodissociation cross sections and with semiclassical calculations of absorption coefficients. Special attention is paid to the investigation of the relative contributions of the H 2 + and H - ions to the total absorption in a wide range of wavelengths and temperatures

The effect of antibiotics on diatom communities

Digital Repository Service at National Institute of Oceanography (India)

DeCosta, P.M.; Anil, A.C.

Effect of antibiotics (penicillin (P), streptomycin (S) and chloramphenicol (C)) on benthic diatom communities was evaluated using a modified extinction–dilution method. The high antibiotic combinations (2PSC and PSC) reduced diatoms by 99...

Infrared spectra of small molecular ions trapped in solid neon

Energy Technology Data Exchange (ETDEWEB)

Jacox, Marilyn E. [Optical Technology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899 (United States)

2015-01-22

The infrared spectrum of a molecular ion provides a unique signature for that species, gives information on its structure, and is amenable to remote sensing. It also serves as a comparison standard for refining ab initio calculations. Experiments in this laboratory trap molecular ions in dilute solid solution in neon at 4.2 K in sufficient concentration for observation of their infrared spectra between 450 and 4000 cm{sup !1}. Discharge-excited neon atoms produce cations by photoionization and/or Penning ionization of the parent molecule. The resulting electrons are captured by other molecules, yielding anions which provide for overall charge neutrality of the deposit. Recent observations of ions produced from C{sub 2}H{sub 4} and BF{sub 3} will be discussed. Because of their relatively large possibility of having low-lying excited electronic states, small, symmetric molecular cations are especially vulnerable to breakdown of the Born-Oppenheimer approximation. Some phenomena which can result from this breakdown will be discussed. Ion-molecule reaction rates are sufficiently high that in some systems absorptions of dimer cations and anions are also observed. When H{sub 2} is introduced into the system, the initially-formed ion may react with it. Among the species resulting from such ion-molecule reactions that have recently been studied are O{sub 4}{sup +}, NH{sub 4}{sup +}, HOCO{sup +}, and HCO{sub 2}{sup !}.

Preparation and coherent manipulation of pure quantum states of a single molecular ion

Science.gov (United States)

Chou, Chin-Wen; Kurz, Christoph; Hume, David B.; Plessow, Philipp N.; Leibrandt, David R.; Leibfried, Dietrich

2017-05-01

Laser cooling and trapping of atoms and atomic ions has led to advances including the observation of exotic phases of matter, the development of precision sensors and state-of-the-art atomic clocks. The same level of control in molecules could also lead to important developments such as controlled chemical reactions and sensitive probes of fundamental theories, but the vibrational and rotational degrees of freedom in molecules pose a challenge for controlling their quantum mechanical states. Here we use quantum-logic spectroscopy, which maps quantum information between two ion species, to prepare and non-destructively detect quantum mechanical states in molecular ions. We develop a general technique for optical pumping and preparation of the molecule into a pure initial state. This enables us to observe high-resolution spectra in a single ion (CaH+) and coherent phenomena such as Rabi flopping and Ramsey fringes. The protocol requires a single, far-off-resonant laser that is not specific to the molecule, so many other molecular ions, including polyatomic species, could be treated using the same methods in the same apparatus by changing the molecular source. Combined with the long interrogation times afforded by ion traps, a broad range of molecular ions could be studied with unprecedented control and precision. Our technique thus represents a critical step towards applications such as precision molecular spectroscopy, stringent tests of fundamental physics, quantum computing and precision control of molecular dynamics.

Dissociative recombination of molecular ions H2+

International Nuclear Information System (INIS)

Abarenov, A.V.; Marchenko, V.S.

1989-01-01

The total cross sections of dissociation and dissociative recombination of slow electrons and molecular ions H 2 + have been calculated in terms of the quasiclassical and dipole approximations. In the calculations allowance was made for the quantum nature of vibrational motion of heavy particles and presence of autoionization of divergence states of the H 2 (Σ u , nl) molecules. It is shown that the H 2 + ion dissociation cross sections are dominant in increase of the electron energy in the ε >or approx. 2-3 eV region for H 2 + (v) ion distribution over the vibrational levels characteristic for the beam experiments. 15 refs.; 5 figs

Atomic hydrogen and diatomic titanium-monoxide molecular spectroscopy in laser-induced plasma

Science.gov (United States)

Parigger, Christian G.; Woods, Alexander C.

2017-03-01

This article gives a brief review of experimental studies of hydrogen Balmer series emission spectra. Ongoing research aims to evaluate early plasma evolution following optical breakdown in laboratory air. Of interest is as well laser ablation of metallic titanium and characterization of plasma evolution. Emission of titanium monoxide is discussed together with modeling of diatomic spectra to infer temperature. The behavior of titanium particles in plasma draws research interests ranging from the modeling of stellar atmospheres to the enhancement of thin film production via pulsed laser deposition.

Fabrication of insulator nanocapillaries from diatoms

International Nuclear Information System (INIS)

Bereczky, R.J.; Tokesi, K.

2006-01-01

Complete text of publication follows. Diatoms are unicellular microscopic organisms with silicon-dioxide based skeleton enveloped with an organic material, which composes essentially polysaccharides and proteins (see Fig. 1a.). As it was shown, the valva of the diatoms build up almost from clean silicondioxide [1]. Therefore, removing the organic compounds from the diatom, we can have in our hand an ideal, about 100 μ m-sized, and almost cylindrical shaped insulating nanostructure. There are various techniques available to disembarrass the diatom from its organic compounds. We used the so called hydrogen peroxide method. The advantageous properties of this method are the followings: a) this is one of the fastest procedures among the possible methods, b) do not require special equipment, c) cheap, and last but not least it is less harmful for health compared to other methods. This procedure can be an alternative way of the fabrication of insulator nanocapillaries. In this case the preparation of the nanocapillaries is simple and quick. Moreover, we do not need to invest expensive special techniques, (like micromachining-, electrochemical etching technique, moulding process etc) as it was necessary for the case of previously developed method producing insulator nanocapillaries [2,3]. Fig. 1b and Fig. 1c. show the scanning electron micrograph of the skeleton of the diatoms. The size of the cylindrical holes are roughly 200 nm (see Fig. 1c). (author)

Electron-impact excitation of diatomic hydride cations II: OH+ and SH+

Science.gov (United States)

Hamilton, James R.; Faure, Alexandre; Tennyson, Jonathan

2018-05-01

R-matrix calculations combined with the adiabatic-nuclei-rotation and Coulomb-Born approximations are used to compute electron-impact rotational rate coefficients for two open-shell diatomic cations of astrophysical interest: the hydoxyl and sulphanyl ions, OH+ and SH+. Hyperfine resolved rate coefficients are deduced using the infinite-order-sudden approximation. The propensity rule ΔF = Δj = ΔN = ±1 is observed, as is expected for cations with a large dipole moment. A model for OH+ excitation in the Orion Bar photon-dominated region is presented which nicely reproduces Herschel observations for an electron fraction xe = 10-4 and an OH+ column density of 3 × 1013 cm-2. Electron-impact electronic excitation cross-sections and rate coefficients for the ions are also presented.

Current trends to comprehend lipid metabolism in diatoms.

Science.gov (United States)

Zulu, Nodumo Nokulunga; Zienkiewicz, Krzysztof; Vollheyde, Katharina; Feussner, Ivo

2018-04-01

Diatoms are the most dominant phytoplankton species in oceans and they continue to receive a great deal of attention because of their significant contributions in ecosystems and the environment. Due to triacylglycerol (TAG) profiles that are abundant in medium-chain fatty acids, diatoms have emerged to be better feed stocks for biofuel production, in comparison to the commonly studied green microalgal species (chlorophytes). Importantly, diatoms are also known for their high levels of the essential ω3 fatty acids, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) and are considered to be a promising alternative source of these components. The two most commonly exploited diatoms include Thalassiosira pseudonana and Phaeodactylum tricornutum. Although obvious similarities between diatoms and chlorophytes exist, there are some substantial differences in their lipid metabolism. This review provides an overview on lipid metabolism in diatoms, with P. tricornutum as the most explored model. Special emphasis is placed on the synthesis and incorporation of very long chain ω3 fatty acids into lipids. Furthermore, current approaches including genetic engineering and biotechnological methods aimed at improving and maximizing lipid production in P. tricornutum are also discussed. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Molecular Characterisation and Co-cultivation of Bacterial Biofilm Communities Associated with the Mat-Forming Diatom Didymosphenia geminata.

Science.gov (United States)

Brandes, Josephin; Kuhajek, Jeanne M; Goodwin, Eric; Wood, Susanna A

2016-10-01

Didymosphenia geminata (Lyngbye) M. Schmidt is a stalked freshwater diatom that is expanding its range globally. In some rivers, D. geminata forms thick and expansive polysaccharide-dominated mats. Like other stalked diatoms, D. geminata cells attach to the substratum with a pad of adhesive extracellular polymeric substance. Research on D. geminata and other diatoms suggests that bacterial biofilm composition may contribute to successful attachment. The aim of this study was to investigate the composition and role of bacterial biofilm communities in D. geminata attachment and survival. Bacterial biofilms were collected at four sites in the main stem of a river (containing D. geminata) and in four tributaries (free of D. geminata). Samples were characterised using automated rRNA intergenic spacer analysis and high-throughput sequencing (HTS). Mat-associated bacteria were isolated and their effect on the early establishment of D. geminata cells assessed using co-culturing experiments. ARISA and HTS data showed differences in bacterial communities between samples with and without D. geminata at two of the four sites. Samples with D. geminata had a higher relative abundance of Sphingobacteria (p geminata reduced survival (p geminata. Attachment was enhanced by Micrococcus sp. and Pseudomonas sp. (p geminata, and may partly explain observed distribution patterns.

Ejection dynamics of hydrogen molecular ions from methanol in intense laser fields

International Nuclear Information System (INIS)

Okino, T; Furukawa, Y; Liu, P; Ichikawa, T; Itakura, R; Hoshina, K; Yamanouchi, K; Nakano, H

2006-01-01

The ejection of hydrogen molecular ions from two-body Coulomb explosion processes of methanol (CH 3 OH, CD 3 OH and CH 3 OD) in an intense laser field (800 nm, 60 fs, 0.2 PW cm -2 ) is investigated by a coincidence momentum imaging method. From the coincidence momentum maps, the ejection processes of hydrogen molecular ions, CH 3 OH 2+ → H m + + CH (3-m) OH + (m = 2, 3), CD 3 OH 2+ → D m + + CH (3-m) OH + (m = 2, 3) and CH 3 OD 2+ → H m + + CH (3-m) OD + (m = 2, 3), are identified. Based on the results obtained with isotopically substituted methanol, the isotope effect on the ejection process of hydrogen molecular ions is discussed. Furthermore, the ejection of H/D exchanged hydrogen molecular ions (HD + , HD 2 + and H 2 D + ) is identified, and the timescales for the H/D exchanging processes are estimated from the extent of anisotropy in the ejection directions

Chronic Iron Limitation Confers Transient Resistance to Oxidative Stress in Marine Diatoms.

Science.gov (United States)

Graff van Creveld, Shiri; Rosenwasser, Shilo; Levin, Yishai; Vardi, Assaf

2016-10-01

Diatoms are single-celled, photosynthetic, bloom-forming algae that are responsible for at least 20% of global primary production. Nevertheless, more than 30% of the oceans are considered "ocean deserts" due to iron limitation. We used the diatom Phaeodactylum tricornutum as a model system to explore diatom's response to iron limitation and its interplay with susceptibility to oxidative stress. By analyzing physiological parameters and proteome profiling, we defined two distinct phases: short-term (chronic (>5 d, phase II) iron limitation. While at phase I no significant changes in physiological parameters were observed, molecular markers for iron starvation, such as Iron Starvation Induced Protein and flavodoxin, were highly up-regulated. At phase II, down-regulation of numerous iron-containing proteins was detected in parallel to reduction in growth rate, chlorophyll content, photosynthetic activity, respiration rate, and antioxidant capacity. Intriguingly, while application of oxidative stress to phase I and II iron-limited cells similarly oxidized the reduced glutathione (GSH) pool, phase II iron limitation exhibited transient resistance to oxidative stress, despite the down regulation of many antioxidant proteins. By comparing proteomic profiles of P. tricornutum under iron limitation and metatranscriptomic data of an iron enrichment experiment conducted in the Pacific Ocean, we propose that iron-limited cells in the natural environment resemble the phase II metabolic state. These results provide insights into the trade-off between optimal growth rate and susceptibility to oxidative stress in the response of diatoms to iron quota in the marine environment. © 2016 American Society of Plant Biologists. All Rights Reserved.

Applications of Diatoms as Potential Microalgae in Nanobiotechnology

OpenAIRE

Ahmad Yari Khosroushahi; Miguel de la Guardia; Mohamad Moradi Ghorakhlu; Ali Akbar Jamali; Fariba Akbari

2012-01-01

Introduction: Diatoms are single cell eukaryotic microalgae, which present in nearly every water habitat make them ideal tools for a wide range of applications such as oil explora­tion, forensic examination, environmental indication, biosilica pattern generation, toxicity testing and eutrophication of aqueous ecosystems. Methods: Essential information on diatoms were reviewed and discussed towards impacts of diatoms on biosynthesis and bioremediation. Results: In this review, we present the ...

Inorganic carbon availability in benthic diatom communities: photosynthesis and migration.

Science.gov (United States)

Marques da Silva, Jorge; Cruz, Sónia; Cartaxana, Paulo

2017-09-05

Diatom-dominated microphytobenthos (MPB) is the main primary producer of many intertidal and shallow subtidal environments, being therefore of critical importance to estuarine and coastal food webs. Owing to tidal cycles, intertidal MPB diatoms are subjected to environmental conditions far more variable than the ones experienced by pelagic diatoms (e.g. light, temperature, salinity, desiccation and nutrient availability). Nevertheless, benthic diatoms evolved adaptation mechanisms to these harsh conditions, including the capacity to move within steep physical and chemical gradients, allowing them to perform photosynthesis efficiently. In this contribution, we will review present knowledge on the effects of dissolved inorganic carbon (DIC) availability on photosynthesis and productivity of diatom-dominated MPB. We present evidence of carbon limitation of photosynthesis in benthic diatom mats and highly productive MPB natural communities. Furthermore, we hypothesize that active vertical migration of epipelic motile diatoms could overcome local depletion of DIC in the photic layer, providing the cells alternately with light and inorganic carbon supply. The few available longer-term experiments on the effects of inorganic carbon enrichment on the productivity of diatom-dominated MPB have yielded inconsistent results. Therefore, further studies are needed to properly assess the response of MPB communities to increased CO 2 and ocean acidification related to climate change.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Author(s).

Improving the Molecular Ion Signal Intensity for In Situ Liquid SIMS Analysis.

Science.gov (United States)

Zhou, Yufan; Yao, Juan; Ding, Yuanzhao; Yu, Jiachao; Hua, Xin; Evans, James E; Yu, Xiaofei; Lao, David B; Heldebrant, David J; Nune, Satish K; Cao, Bin; Bowden, Mark E; Yu, Xiao-Ying; Wang, Xue-Lin; Zhu, Zihua

2016-12-01

In situ liquid secondary ion mass spectrometry (SIMS) enabled by system for analysis at the liquid vacuum interface (SALVI) has proven to be a promising new tool to provide molecular information at solid-liquid and liquid-vacuum interfaces. However, the initial data showed that useful signals in positive ion spectra are too weak to be meaningful in most cases. In addition, it is difficult to obtain strong negative molecular ion signals when m/z>200. These two drawbacks have been the biggest obstacle towards practical use of this new analytical approach. In this study, we report that strong and reliable positive and negative molecular signals are achievable after optimizing the SIMS experimental conditions. Four model systems, including a 1,8-diazabicycloundec-7-ene (DBU)-base switchable ionic liquid, a live Shewanella oneidensis biofilm, a hydrated mammalian epithelia cell, and an electrolyte popularly used in Li ion batteries were studied. A signal enhancement of about two orders of magnitude was obtained in comparison with non-optimized conditions. Therefore, molecular ion signal intensity has become very acceptable for use of in situ liquid SIMS to study solid-liquid and liquid-vacuum interfaces. Graphical Abstract ᅟ.

The molecular dynamics simulation of ion-induced ripple growth

International Nuclear Information System (INIS)

Suele, P.; Heinig, K.-H.

2009-01-01

The wavelength-dependence of ion-sputtering induced growth of repetitive nanostructures, such as ripples has been studied by molecular dynamics (MD) simulations in Si. The early stage of the ion erosion driven development of ripples has been simulated on prepatterned Si stripes with a wavy surface. The time evolution of the height function and amplitude of the sinusoidal surface profile has been followed by simulated ion-sputtering. According to Bradley-Harper (BH) theory, we expect correlation between the wavelength of ripples and the stability of them. However, we find that in the small ripple wavelength (λ) regime BH theory fails to reproduce the results obtained by molecular dynamics. We find that at short wavelengths (λ 35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in λ long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for λ>35 nm ripples. In another words, ripples in the long wavelength limit seems to be stable against ion-sputtering. A qualitative comparison of our simulation results with recent experimental data on nanopatterning under irradiation is attempted.

Identifying metabolic pathways for production of extracellular polymeric substances by the diatom Fragilariopsis cylindrus inhabiting sea ice.

Science.gov (United States)

Aslam, Shazia N; Strauss, Jan; Thomas, David N; Mock, Thomas; Underwood, Graham J C

2018-05-01

Diatoms are significant primary producers in sea ice, an ephemeral habitat with steep vertical gradients of temperature and salinity characterizing the ice matrix environment. To cope with the variable and challenging conditions, sea ice diatoms produce polysaccharide-rich extracellular polymeric substances (EPS) that play important roles in adhesion, cell protection, ligand binding and as organic carbon sources. Significant differences in EPS concentrations and chemical composition corresponding to temperature and salinity gradients were present in sea ice from the Weddell Sea and Eastern Antarctic regions of the Southern Ocean. To reconstruct the first metabolic pathway for EPS production in diatoms, we exposed Fragilariopsis cylindrus, a key bi-polar diatom species, to simulated sea ice formation. Transcriptome profiling under varying conditions of EPS production identified a significant number of genes and divergent alleles. Their complex differential expression patterns under simulated sea ice formation was aligned with physiological and biochemical properties of the cells, and with field measurements of sea ice EPS characteristics. Thus, the molecular complexity of the EPS pathway suggests metabolic plasticity in F. cylindrus is required to cope with the challenging conditions of the highly variable and extreme sea ice habitat.

Potential of diatom consortium developed by nutrient enrichment for biodiesel production and simultaneous nutrient removal from waste water.

Science.gov (United States)

Marella, Thomas Kiran; Parine, Narasimha Reddy; Tiwari, Archana

2018-05-01

Because of the decreasing fossil fuel supply and increasing greenhouse gas (GHG) emissions, microalgae have been identified as a viable and sustainable feedstock for biofuel production. The major effect of the release of wastewater rich in organic compounds has led to the eutrophication of freshwater ecosystems. A combined approach of freshwater diatom cultivation with urban sewage water treatment is a promising solution for nutrient removal and biofuel production. In this study, urban wastewater from eutrophic Hussain Sagar Lake was used to cultivate a diatom algae consortium, and the effects of silica and trace metal enrichment on growth, nutrient removal, and lipid production were evaluated. The nano-silica-based micronutrient mixture Nualgi containing Si, Fe, and metal ions was used to optimize diatom growth. Respectively, N and P reductions of 95.1% and 88.9%, COD and BOD reductions of 91% and 51% with a biomass yield of 122.5 mg L -1  day -1 and lipid productivity of 37 mg L -1  day -1 were observed for cultures grown in waste water using Nualgi. Fatty acid profiles revealed 13 different fatty acids with slight differences in their percentage of dry cell weight (DCW) depending on enrichment level. These results demonstrate the potential of diatom algae grown in wastewater to produce feedstock for renewable biodiesel production. Enhanced carbon and excess nutrient utilization makes diatoms ideal candidates for co-processes such as CO 2 sequestration, biodiesel production, and wastewater phycoremediation.

He2+ molecular ion and the He- atomic ion in strong magnetic fields

Science.gov (United States)

Vieyra, J. C. Lopez; Turbiner, A. V.

2017-08-01

We study the question of existence, i.e., stability with respect to dissociation of the spin-quartet permutation- and reflection-symmetric 4(-3) +g (Sz=-3 /2 ,M =-3 ) state of the (α α e e e ) Coulomb system: the He2 + molecular ion, placed in a magnetic field 0 ≤B ≤10 000 a.u. We assume that the α particles are infinitely massive (Born-Oppenheimer approximation of zero order) and adopt the parallel configuration, when the molecular axis and the magnetic field direction coincide, as the optimal configuration. The study of the stability is performed variationally with a physically adequate trial function. To achieve this goal, we explore several helium-containing compounds in strong magnetic fields, in particular; we study the spin-quartet ground state of the He- ion and the ground (spin-triplet) state of the helium atom, both for a magnetic field in 100 ≤B ≤10 000 a.u. The main result is that the He2 + molecular ion in the state 4(-3) +g is stable towards all possible decay modes for magnetic fields B ≳120 a .u . and with the magnetic field increase the ion becomes more tightly bound and compact with a cigar-type form of electronic cloud. At B =1000 a .u . , the dissociation energy of He2 + into He-+α is ˜702 eV and the dissociation energy for the decay channel to He +α +e is ˜729 eV , and both energies are in the energy window for one of the observed absorption features of the isolated neutron star 1E1207.4-5209.

A molecular-gap device for specific determination of mercury ions

Science.gov (United States)

Guo, Zheng; Liu, Zhong-Gang; Yao, Xian-Zhi; Zhang, Kai-Sheng; Chen, Xing; Liu, Jin-Huai; Huang, Xing-Jiu

2013-11-01

Specific determination/monitoring of trace mercury ions (Hg2+) in environmental water is of significant importance for drinking safety. Complementarily to conventional inductively coupled plasma mass spectrometry and atomic emission/absorption spectroscopy, several methods, i.e., electrochemical, fluorescent, colorimetric, and surface enhanced Raman scattering approaches, have been developed recently. Despite great success, many inevitably encounter the interferences from other metal ions besides the complicated procedures and sophisticated equipments. Here we present a molecular-gap device for specific determination of trace Hg2+ in both standardized solutions and environmental samples based on conductivity-modulated glutathione dimer. Through a self-assembling technique, a thin film of glutathione monolayer capped Au nanoparticles is introduced into 2.5 μm-gap-electrodes, forming numerous double molecular layer gaps. Notably, the fabricated molecular-gap device shows a specific response toward Hg2+ with a low detection limit actually measured down to 1 nM. Theoretical calculations demonstrate that the specific sensing mechanism greatly depends on the electron transport ability of glutathione dimer bridged by heavy metal ions, which is determined by its frontier molecular orbital, not the binding energy.

A caveat regarding diatom-inferred nitrogen concentrations in oligotrophic lakes

Science.gov (United States)

Arnett, Heather A.; Saros, Jasmine E.; Mast, M. Alisa

2012-01-01

Atmospheric deposition of reactive nitrogen (Nr) has enriched oligotrophic lakes with nitrogen (N) in many regions of the world and elicited dramatic changes in diatom community structure. The lakewater concentrations of nitrate that cause these community changes remain unclear, raising interest in the development of diatom-based transfer functions to infer nitrate. We developed a diatom calibration set using surface sediment samples from 46 high-elevation lakes across the Rocky Mountains of the western US, a region spanning an N deposition gradient from very low to moderate levels (phosphorus, and hypolimnetic water temperature were related to diatom distributions. A transfer function was developed for nitrate and applied to a sedimentary diatom profile from Heart Lake in the central Rockies. The model coefficient of determination (bootstrapping validation) of 0.61 suggested potential for diatom-inferred reconstructions of lakewater nitrate concentrations over time, but a comparison of observed versus diatom-inferred nitrate values revealed the poor performance of this model at low nitrate concentrations. Resource physiology experiments revealed that nitrogen requirements of two key taxa were opposite to nitrate optima defined in the transfer function. Our data set reveals two underlying ecological constraints that impede the development of nitrate transfer functions in oligotrophic lakes: (1) even in lakes with nitrate concentrations below quantification (<1 μg L−1), diatom assemblages were already dominated by species indicative of moderate N enrichment; (2) N-limited oligotrophic lakes switch to P limitation after receiving only modest inputs of reactive N, shifting the controls on diatom species changes along the length of the nitrate gradient. These constraints suggest that quantitative inferences of nitrate from diatom assemblages will likely require experimental approaches.

Photosynthetic Pigments in Diatoms.

Science.gov (United States)

Kuczynska, Paulina; Jemiola-Rzeminska, Malgorzata; Strzalka, Kazimierz

2015-09-16

Photosynthetic pigments are bioactive compounds of great importance for the food, cosmetic, and pharmaceutical industries. They are not only responsible for capturing solar energy to carry out photosynthesis, but also play a role in photoprotective processes and display antioxidant activity, all of which contribute to effective biomass and oxygen production. Diatoms are organisms of a distinct pigment composition, substantially different from that present in plants. Apart from light-harvesting pigments such as chlorophyll a, chlorophyll c, and fucoxanthin, there is a group of photoprotective carotenoids which includes β-carotene and the xanthophylls, diatoxanthin, diadinoxanthin, violaxanthin, antheraxanthin, and zeaxanthin, which are engaged in the xanthophyll cycle. Additionally, some intermediate products of biosynthetic pathways have been identified in diatoms as well as unusual pigments, e.g., marennine. Marine algae have become widely recognized as a source of unique bioactive compounds for potential industrial, pharmaceutical, and medical applications. In this review, we summarize current knowledge on diatom photosynthetic pigments complemented by some new insights regarding their physico-chemical properties, biological role, and biosynthetic pathways, as well as the regulation of pigment level in the cell, methods of purification, and significance in industries.

Photosynthetic Pigments in Diatoms

Directory of Open Access Journals (Sweden)

Paulina Kuczynska

2015-09-01

Full Text Available Photosynthetic pigments are bioactive compounds of great importance for the food, cosmetic, and pharmaceutical industries. They are not only responsible for capturing solar energy to carry out photosynthesis, but also play a role in photoprotective processes and display antioxidant activity, all of which contribute to effective biomass and oxygen production. Diatoms are organisms of a distinct pigment composition, substantially different from that present in plants. Apart from light-harvesting pigments such as chlorophyll a, chlorophyll c, and fucoxanthin, there is a group of photoprotective carotenoids which includes β-carotene and the xanthophylls, diatoxanthin, diadinoxanthin, violaxanthin, antheraxanthin, and zeaxanthin, which are engaged in the xanthophyll cycle. Additionally, some intermediate products of biosynthetic pathways have been identified in diatoms as well as unusual pigments, e.g., marennine. Marine algae have become widely recognized as a source of unique bioactive compounds for potential industrial, pharmaceutical, and medical applications. In this review, we summarize current knowledge on diatom photosynthetic pigments complemented by some new insights regarding their physico-chemical properties, biological role, and biosynthetic pathways, as well as the regulation of pigment level in the cell, methods of purification, and significance in industries.

Epibiotic Diatoms Are Universally Present on All Sea Turtle Species

Science.gov (United States)

Majewska, Roksana; Lazo-Wasem, Eric A.; Nel, Ronel; Paladino, Frank V.; Rojas, Lourdes; Zardus, John D.; Pinou, Theodora

2016-01-01

The macro-epibiotic communities of sea turtles have been subject to growing interest in recent years, yet their micro-epibiotic counterparts are almost entirely unknown. Here, we provide the first evidence that diatoms are epibionts for all seven extant species of sea turtle. Using Scanning Electron Microscopy, we inspected superficial carapace or skin samples from a single representative of each turtle species. We distinguished 18 diatom taxa from these seven individuals, with each sea turtle species hosting at least two diatom taxa. We recommend that future research is undertaken to confirm whether diatom communities vary between sea turtle species and whether these diatom taxa are facultative or obligate commensals. PMID:27257972

Rotational Laser Cooling of Vibrationally and Translationally Cold Molecular Ions

DEFF Research Database (Denmark)

Drewsen, Michael

2011-01-01

an excellent alternative to atomic qubits in the realization of a practical ion trap based quantum computer due to favourable internal state decoherence rates. In chemistry, state prepared molecular targets are an ideal starting point for uni-molecular reactions, including coherent control...... of photofragmentation through the application of various laser sources [5,6]. In cold bi-molecular reactions, where the effect of even tiny potential barriers becomes significant, experiments with state prepared molecules can yield important information on the details of the potential curves of the molecular complexes...... by sympathetic cooling with Doppler laser cooled Mg+ ions. Giving the time for the molecules to equilibrate internally to the room temperature blackbody radiation, the vibrational degree of freedom will freeze out, leaving only the rotational degree of freedom to be cooled. We report here on the implementation...

Responses of diatom communities to hydrological processes during rainfall events

Science.gov (United States)

Wu, Naicheng; Faber, Claas; Ulrich, Uta; Fohrer, Nicola

2015-04-01

The importance of diatoms as a tracer of hydrological processes has been recently recognized (Pfister et al. 2009, Pfister et al. 2011, Tauro et al. 2013). However, diatom variations in a short-term scale (e.g., sub-daily) during rainfall events have not been well documented yet. In this study, rainfall event-based diatom samples were taken at the outlet of the Kielstau catchment (50 km2), a lowland catchment in northern Germany. A total of nine rainfall events were caught from May 2013 to April 2014. Non-metric multidimensional scaling (NMDS) revealed that diatom communities of different events were well separated along NMDS axis I and II, indicating a remarkable temporal variation. By correlating water level (a proxy of discharge) and different diatom indices, close relationships were found. For example, species richness, biovolume (μm3), Shannon diversity and moisture index01 (%, classified according to van Dam et al. 1994) were positively related with water level at the beginning phase of the rainfall (i.e. increasing limb of discharge peak). However, in contrast, during the recession limb of the discharge peak, diatom indices showed distinct responses to water level declines in different rainfall events. These preliminary results indicate that diatom indices are highly related to hydrological processes. The next steps will include finding out the possible mechanisms of the above phenomena, and exploring the contributions of abiotic variables (e.g., hydrologic indices, nutrients) to diatom community patterns. Based on this and ongoing studies (Wu et al. unpublished data), we will incorporate diatom data into End Member Mixing Analysis (EMMA) and select the tracer set that is best suited for separation of different runoff components in our study catchment. Keywords: Diatoms, Rainfall event, Non-metric multidimensional scaling, Hydrological process, Indices References: Pfister L, McDonnell JJ, Wrede S, Hlúbiková D, Matgen P, Fenicia F, Ector L, Hoffmann L

Synthetic Ion Channels and DNA Logic Gates as Components of Molecular Robots.

Science.gov (United States)

Kawano, Ryuji

2018-02-19

A molecular robot is a next-generation biochemical machine that imitates the actions of microorganisms. It is made of biomaterials such as DNA, proteins, and lipids. Three prerequisites have been proposed for the construction of such a robot: sensors, intelligence, and actuators. This Minireview focuses on recent research on synthetic ion channels and DNA computing technologies, which are viewed as potential candidate components of molecular robots. Synthetic ion channels, which are embedded in artificial cell membranes (lipid bilayers), sense ambient ions or chemicals and import them. These artificial sensors are useful components for molecular robots with bodies consisting of a lipid bilayer because they enable the interface between the inside and outside of the molecular robot to function as gates. After the signal molecules arrive inside the molecular robot, they can operate DNA logic gates, which perform computations. These functions will be integrated into the intelligence and sensor sections of molecular robots. Soon, these molecular machines will be able to be assembled to operate as a mass microrobot and play an active role in environmental monitoring and in vivo diagnosis or therapy. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Oceanographic and Biogeochemical Insights from Diatom Genomes

Science.gov (United States)

Bowler, Chris; Vardi, Assaf; Allen, Andrew E.

2010-01-01

Diatoms are the most successful group of eukaryotic phytoplankton in the modern ocean and have risen to dominance relatively quickly over the last 100 million years. Recently completed whole genome sequences from two species of diatom, Thalassiosira pseudonana and Phaeodactylum tricornutum, have revealed a wealth of information about the evolutionary origins and metabolic adaptations that have led to their ecological success. A major finding is that they have incorporated genes both from their endosymbiotic ancestors and by horizontal gene transfer from marine bacteria. This unique melting pot of genes encodes novel capacities for metabolic management, for example, allowing the integration of a urea cycle into a photosynthetic cell. In this review we show how genome-enabled approaches are being leveraged to explore major phenomena of oceanographic and biogeochemical relevance, such as nutrient assimilation and life histories in diatoms. We also discuss how diatoms may be affected by climate change-induced alterations in ocean processes.

Molecular dynamics simulations of ion range profiles for heavy ions in light targets

Energy Technology Data Exchange (ETDEWEB)

Lan, C. [Department of Materials Science and Engineering, University of Tennessee, Knoxville, TN 37996 (United States); State Key Laboratory of Nuclear Physics and Technology, Peking University, 100871 (China); Xue, J.M. [State Key Laboratory of Nuclear Physics and Technology, Peking University, 100871 (China); Zhang, Y., E-mail: Zhangy1@ornl.gov [Department of Materials Science and Engineering, University of Tennessee, Knoxville, TN 37996 (United States); Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States); Morris, J.R. [Department of Materials Science and Engineering, University of Tennessee, Knoxville, TN 37996 (United States); Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States); Zhu, Z. [Pacific Northwest National Laboratory, Richland, WA 99352 (United States); Gao, Y.; Wang, Y.G.; Yan, S. [State Key Laboratory of Nuclear Physics and Technology, Peking University, 100871 (China); Weber, W.J. [Department of Materials Science and Engineering, University of Tennessee, Knoxville, TN 37996 (United States); Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States)

2012-09-01

The determination of stopping powers for slow heavy ions in targets containing light elements is important to accurately describe ion-solid interactions, evaluate ion irradiation effects and predict ion ranges for device fabrication and nuclear applications. Recently, discrepancies of up to 40% between the experimental results and SRIM (Stopping and Range of Ions in Matter) predictions of ion ranges for heavy ions with medium and low energies (<{approx}25 keV/nucleon) in light elemental targets have been reported. The longer experimental ion ranges indicate that the stopping powers used in the SRIM code are overestimated. Here, a molecular dynamics simulation scheme is developed to calculate the ion ranges of heavy ions in light elemental targets. Electronic stopping powers generated from both a reciprocity approach and the SRIM code are used to investigate the influence of electronic stopping on ion range profiles. The ion range profiles for Au and Pb ions in SiC and Er ions in Si, with energies between 20 and 5250 keV, are simulated. The simulation results show that the depth profiles of implanted ions are deeper and in better agreement with the experiments when using the electronic stopping power values derived from the reciprocity approach. These results indicate that the origin of the discrepancy in ion ranges between experimental results and SRIM predictions in the low energy region may be an overestimation of the electronic stopping powers used in SRIM.

Investigation of the silicon ion density during molecular beam epitaxy growth

CERN Document Server

Eifler, G; Ashurov, K; Morozov, S

2002-01-01

Ions impinging on a surface during molecular beam epitaxy influence the growth and the properties of the growing layer, for example, suppression of dopant segregation and the generation of crystal defects. The silicon electron gun in the molecular beam epitaxy (MBE) equipment is used as a source for silicon ions. To use the effect of ion bombardment the mechanism of generation and distribution of ions was investigated. A monitoring system was developed and attached at the substrate position in the MBE growth chamber to measure the ion and electron densities towards the substrate. A negative voltage was applied to the substrate to modify the ion energy and density. Furthermore the current caused by charge carriers impinging on the substrate was measured and compared with the results of the monitoring system. The electron and ion densities were measured by varying the emission current of the e-gun achieving silicon growth rates between 0.07 and 0.45 nm/s and by changing the voltage applied to the substrate betw...

Physics with fast molecular-ion beams. Proceedings of workshop held at Argonne National Laboratory, August 20-21, 1979

International Nuclear Information System (INIS)

Gemmell, D.S.

1979-01-01

The Workshop on Physics with Fast Molecular-Ion Beams was held in the Physics Division, Argonne National Laboratory on August 20 and 21, 1979. The meeting brought together representatives from several groups studying the interactions of fast (MeV) molecular-ion beams with matter. By keeping the Workshop program sharply focussed on current work related to the interactions of fast molecular ions, it was made possible for the participants to engage in vigorous and detailed discussions concerning such specialized topics as molecular-ion dissociation and transmission, wake effects, ionic charge states, cluster stopping powers, beam-foil spectroscopy, electron-emissions studies with molecular-ion beams, and molecular-ion structure determinations

Diatomic interaction potential theory applications

CERN Document Server

Goodisman, Jerry

2013-01-01

Diatomic Interaction Potential Theory, Volume 2: Applications discusses the variety of applicable theoretical material and approaches in the calculations for diatomic systems in their ground states. The volume covers the descriptions and illustrations of modern calculations. Chapter I discusses the calculation of the interaction potential for large and small values of the internuclear distance R (separated and united atom limits). Chapter II covers the methods used for intermediate values of R, which in principle means any values of R. The Hartree-Fock and configuration interaction schemes des

Effects of the oxylipin-producing diatom Skeletonema marinoi on gene expression levels of the calanoid copepod Calanus sinicus.

Science.gov (United States)

Lauritano, Chiara; Carotenuto, Ylenia; Vitiello, Valentina; Buttino, Isabella; Romano, Giovanna; Hwang, Jiang-Shiou; Ianora, Adrianna

2015-12-01

Diatoms are eukaryotic unicellular plants that constitute one of the major components of marine phytoplankton, comprising up to 40% of annual productivity at sea and representing 25% of global carbon-fixation. Diatoms have traditionally been considered a preferential food for zooplankton grazers such as copepods, but, in the last two decades, this beneficial role has been challenged after the discovery that many species of diatoms produce toxic metabolites, collectively termed oxylipins, that induce reproductive failure in zooplankton grazers. Diatoms are the dominant natural diet of Calanus sinicus, a cold-temperate calanoid copepod that supports secondary production of important fisheries in the shelf ecosystems of the Northwest Pacific Ocean, Yellow Sea, Sea of Japan and South China Sea. In this study, the effect of the oxylipin-producing diatom Skeletonema marinoi on C. sinicus has been evaluated by analyzing expression level changes of genes involved in defense and detoxification systems. Results show that C. sinicus is more resistant to a diet of this diatom species in terms of gene expression patterns, compared to the congeneric species Calanus helgolandicus which is an important constituent of the temperate waters of the Atlantic Ocean and northern Mediterranean Sea. These findings contribute to the better understanding of genetic and/or phenotypic flexibility of copepod species and their capabilities to cope with stress by identifying molecular markers (such as stress and detoxification genes) as biosensors for environmental perturbations (e.g. toxins and contaminants) affecting marine copepods. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Micro structure processing on plastics by accelerated hydrogen molecular ions

Science.gov (United States)

Hayashi, H.; Hayakawa, S.; Nishikawa, H.

2017-08-01

A proton has 1836 times the mass of an electron and is the lightest nucleus to be used for accelerator in material modification. We can setup accelerator with the lowest acceleration voltage. It is preferable characteristics of Proton Beam Writer (PBW) for industrial applications. On the contrary ;proton; has the lowest charge among all nuclei and the potential impact to material is lowest. The object of this research is to improve productivity of the PBW for industry application focusing on hydrogen molecular ions. These ions are generated in the same ion source by ionizing hydrogen molecule. There is no specific ion source requested and it is suitable for industrial use. We demonstrated three dimensional (3D) multilevel micro structures on polyester base FPC (Flexible Printed Circuits) using proton, H2+ and H3+. The reactivity of hydrogen molecular ions is much higher than that of proton and coincident with the level of expectation. We can apply this result to make micro devices of 3D multilevel structures on FPC.

Epibiotic Diatoms Are Universally Present on All Sea Turtle Species.

Directory of Open Access Journals (Sweden)

Nathan J Robinson

Full Text Available The macro-epibiotic communities of sea turtles have been subject to growing interest in recent years, yet their micro-epibiotic counterparts are almost entirely unknown. Here, we provide the first evidence that diatoms are epibionts for all seven extant species of sea turtle. Using Scanning Electron Microscopy, we inspected superficial carapace or skin samples from a single representative of each turtle species. We distinguished 18 diatom taxa from these seven individuals, with each sea turtle species hosting at least two diatom taxa. We recommend that future research is undertaken to confirm whether diatom communities vary between sea turtle species and whether these diatom taxa are facultative or obligate commensals.

All New Faces of Diatoms: Potential Source of Nanomaterials and Beyond

Directory of Open Access Journals (Sweden)

Meerambika Mishra

2017-07-01

Full Text Available Nature’s silicon marvel, the diatoms have lately astounded the scientific community with its intricate designs and lasting durability. Diatoms are a major group of phytoplanktons involved in the biogeochemical cycling of silica and are virtually inherent in every environment ranging from water to ice to soil. The usage of diatoms has proved prudently cost effective and its handling neither requires costly materials nor sophisticated instruments. Diatoms can easily be acquired from the environment, their culture requires ambient condition and does not involve any costly media or expensive instruments, besides, they can be transported in small quantities and proliferated to a desirable confluence from that scratch, thus are excellent cost effective industrial raw material. Naturally occurring diatom frustules are a source of nanomaterials. Their silica bio-shells have raised curiosity among nanotechnologists who hope that diatoms will facilitate tailoring minuscule structures which are beyond the capabilities of material scientists. Additionally, there is a colossal diversity in the dimensions of diatoms as the frustule shape differs from species to species; this provides a scope for the choice of a particular species of diatom to be tailored to an exacting requisite, thus paving the way to create desired three dimensional nanocomposites. The present article explores the use of diatoms in various arenas of science, may it be in nanotechnology, biotechnology, environmental science, biophysics or biochemistry and summarizes facets of diatom biology under one umbrella. Special emphasis has been given to biosilicification, biomineralization and use of diatoms as nanomaterials’, drug delivery vehicles, optical and immune-biosensors, filters, immunodiagnostics, aquaculture feeds, lab-on-a-chip, metabolites, and biofuels.

Collisions of antiprotons with hydrogen molecular ions

DEFF Research Database (Denmark)

Lühr, Armin Christian; Saenz, Alejandro

2009-01-01

Time-dependent close-coupling calculations of the ionization and excitation cross section for antiproton collisions with molecular hydrogen ions are performed in an impact energy range from 0.5 keV to 10 MeV. The Born-Oppenheimer and Franck-Condon approximations as well as the impact parameter...

Automated measurement of diatom size

Science.gov (United States)

Spaulding, Sarah A.; Jewson, David H.; Bixby, Rebecca J.; Nelson, Harry; McKnight, Diane M.

2012-01-01

Size analysis of diatom populations has not been widely considered, but it is a potentially powerful tool for understanding diatom life histories, population dynamics, and phylogenetic relationships. However, measuring cell dimensions on a light microscope is a time-consuming process. An alternative technique has been developed using digital flow cytometry on a FlowCAM® (Fluid Imaging Technologies) to capture hundreds, or even thousands, of images of a chosen taxon from a single sample in a matter of minutes. Up to 30 morphological measures may be quantified through post-processing of the high resolution images. We evaluated FlowCAM size measurements, comparing them against measurements from a light microscope. We found good agreement between measurement of apical cell length in species with elongated, straight valves, including small Achnanthidium minutissimum (11-21 µm) and largeDidymosphenia geminata (87–137 µm) forms. However, a taxon with curved cells, Hannaea baicalensis (37–96 µm), showed differences of ~ 4 µm between the two methods. Discrepancies appear to be influenced by the choice of feret or geodesic measurement for asymmetric cells. We describe the operating conditions necessary for analysis of size distributions and present suggestions for optimal instrument conditions for size analysis of diatom samples using the FlowCAM. The increased speed of data acquisition through use of imaging flow cytometers like the FlowCAM is an essential step for advancing studies of diatom populations.

Preparation and method of study of fossil diatoms

Digital Repository Service at National Institute of Oceanography (India)

Setty, M.G.A.P.

Two methods of chemical concentration of diatoms occurring in fresh-water sediments, and one chemico-mechanical method of concentration for diatoms occurring in marine sediments are outlined, with emphasis on the extreme care that needs...

Biomimetic supercontainers for size-selective electrochemical sensing of molecular ions

Science.gov (United States)

Netzer, Nathan L.; Must, Indrek; Qiao, Yupu; Zhang, Shi-Li; Wang, Zhenqiang; Zhang, Zhen

2017-04-01

New ionophores are essential for advancing the art of selective ion sensing. Metal-organic supercontainers (MOSCs), a new family of biomimetic coordination capsules designed using sulfonylcalix[4]arenes as container precursors, are known for their tunable molecular recognition capabilities towards an array of guests. Herein, we demonstrate the use of MOSCs as a new class of size-selective ionophores dedicated to electrochemical sensing of molecular ions. Specifically, a MOSC molecule with its cavities matching the size of methylene blue (MB+), a versatile organic molecule used for bio-recognition, was incorporated into a polymeric mixed-matrix membrane and used as an ion-selective electrode. This MOSC-incorporated electrode showed a near-Nernstian potentiometric response to MB+ in the nano- to micro-molar range. The exceptional size-selectivity was also evident through contrast studies. To demonstrate the practical utility of our approach, a simulated wastewater experiment was conducted using water from the Fyris River (Sweden). It not only showed a near-Nernstian response to MB+ but also revealed a possible method for potentiometric titration of the redox indicator. Our study thus represents a new paradigm for the rational design of ionophores that can rapidly and precisely monitor molecular ions relevant to environmental, biomedical, and other related areas.

THE INFLUENCE OF SUBMERGED MACROPHYTES ON SEDIMENTARY DIATOM ASSEMBLAGES(1).

Science.gov (United States)

Vermaire, Jesse C; Prairie, Yves T; Gregory-Eaves, Irene

2011-12-01

Submerged macrophytes are a central component of lake ecosystems; however, little is known regarding their long-term response to environmental change. We have examined the potential of diatoms as indicators of past macrophyte biomass. We first sampled periphyton to determine whether habitat was a predictor of diatom assemblage. We then sampled 41 lakes in Quebec, Canada, to evaluate whether whole-lake submerged macrophyte biomass (BiomEpiV) influenced surface sediment diatom assemblages. A multivariate regression tree (MRT) was used to construct a semiquantitative model to reconstruct past macrophyte biomass. We determined that periphytic diatom assemblages on macrophytes were significantly different from those on wood and rocks (ANOSIM R = 0.63, P macrophyte, nutrient-limited lakes (BiomEpiV ≥525 μg · L(-1) ; total phosphorus [TP] macrophyte, nutrient-limited lakes (BiomEpiV macrophytes have a significant influence on diatom community structure and that sedimentary diatom assemblages can be used to infer past macrophyte abundance. © 2011 Phycological Society of America.

Electron and molecular ion collisions relevant to divertor plasma

International Nuclear Information System (INIS)

Takagi, H.

2005-01-01

We introduce the concept of the multi-channel quantum defect theory (MQDT) and show the outline of the MQDT newly extended to include the dissociative states. We investigate some molecular processes relevant to the divertor plasma by using the MQDT: the dissociative recombination, dissociative excitation, and rotation-vibrational transition in the hydrogen molecular ion and electron collisions. (author)

Molecular beam studies of ion-molecule reactions

International Nuclear Information System (INIS)

Gentry, W.R.

1978-01-01

A review is presented in which an attempt is made to highlight some of the areas in which molecular beam techniques contribute to the understanding of ion--molecule reaction dynamics. Included are reactant kinetic energy range and resolution, internal state selection and analysis, and new chemical systems and phenomena. 35 references

Genetic and metabolic engineering in diatoms.

Science.gov (United States)

Huang, Weichao; Daboussi, Fayza

2017-09-05

Diatoms have attracted considerable attention due to their success in diverse environmental conditions, which probably is a consequence of their complex origins. Studies of their metabolism will provide insight into their adaptation capacity and are a prerequisite for metabolic engineering. Several years of investigation have led to the development of the genome engineering tools required for such studies, and a profusion of appropriate tools is now available for exploring and exploiting the metabolism of these organisms. Diatoms are highly prized in industrial biotechnology, due to both their richness in natural lipids and carotenoids and their ability to produce recombinant proteins, of considerable value in diverse markets. This review provides an overview of recent advances in genetic engineering methods for diatoms, from the development of gene expression cassettes and gene delivery methods, to cutting-edge genome-editing technologies. It also highlights the contributions of these rapid developments to both basic and applied research: they have improved our understanding of key physiological processes; and they have made it possible to modify the natural metabolism to favour the production of specific compounds or to produce new compounds for green chemistry and pharmaceutical applications.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Author(s).

Ion-beam-induced aggregation in polystyrene: The influence of the molecular parameters

International Nuclear Information System (INIS)

Puglisi, O.; Licciardello, A.; Calcagno, L.; Foti, G.

1988-01-01

The formation of an insoluble gel under ion-beam bombardment is governed by ion-beam parameters and target parameters. Here reported is a study of the influence of the target molecular parameters on the sol--gel transition of ion-bombarded polystyrene with particular emphasis for the number-average molecular weight M-bar/sub n/. It is shown that the main parameter is the number of macromolcules of the film so that by adopting a ''corrected'' fluence F/n (ions per macromolecule), the different curves of the various polymers collapse in only one universal curve. The importance of the ''corrected'' fluence is shown also at molecular level and the MWD of the various polymers is similar at equal F/n values. An experimental model is outlined which explains the sol--gel transition on the basis of transition from an isolated-track regime to an overlap regime where the formation of insoluble giant macromolecules occurs

Isolation and biochemical characterization of underwater adhesives from diatoms.

Science.gov (United States)

Poulsen, Nicole; Kröger, Nils; Harrington, Matthew J; Brunner, Eike; Paasch, Silvia; Buhmann, Matthias T

2014-01-01

Many aquatic organisms are able to colonize surfaces through the secretion of underwater adhesives. Diatoms are unicellular algae that have the capability to colonize any natural and man-made submerged surfaces. There is great technological interest in both mimicking and preventing diatom adhesion, yet the biomolecules responsible have so far remained unidentified. A new method for the isolation of diatom adhesive material is described and its amino acid and carbohydrate composition determined. The adhesive materials from two model diatoms show differences in their amino acid and carbohydrate compositions, but also share characteristic features including a high content of uronic acids, the predominance of hydrophilic amino acid residues, and the presence of 3,4-dihydroxyproline, an extremely rare amino acid. Proteins containing dihydroxyphenylalanine, which mediate underwater adhesion of mussels, are absent. The data on the composition of diatom adhesives are consistent with an adhesion mechanism based on complex coacervation of polyelectrolyte-like biomolecules.

Influence of diatom diversity on the ocean biological carbon pump

Science.gov (United States)

Tréguer, Paul; Bowler, Chris; Moriceau, Brivaela; Dutkiewicz, Stephanie; Gehlen, Marion; Aumont, Olivier; Bittner, Lucie; Dugdale, Richard; Finkel, Zoe; Iudicone, Daniele; Jahn, Oliver; Guidi, Lionel; Lasbleiz, Marine; Leblanc, Karine; Levy, Marina; Pondaven, Philippe

2018-01-01

Diatoms sustain the marine food web and contribute to the export of carbon from the surface ocean to depth. They account for about 40% of marine primary productivity and particulate carbon exported to depth as part of the biological pump. Diatoms have long been known to be abundant in turbulent, nutrient-rich waters, but observations and simulations indicate that they are dominant also in meso- and submesoscale structures such as fronts and filaments, and in the deep chlorophyll maximum. Diatoms vary widely in size, morphology and elemental composition, all of which control the quality, quantity and sinking speed of biogenic matter to depth. In particular, their silica shells provide ballast to marine snow and faecal pellets, and can help transport carbon to both the mesopelagic layer and deep ocean. Herein we show that the extent to which diatoms contribute to the export of carbon varies by diatom type, with carbon transfer modulated by the Si/C ratio of diatom cells, the thickness of the shells and their life strategies; for instance, the tendency to form aggregates or resting spores. Model simulations project a decline in the contribution of diatoms to primary production everywhere outside of the Southern Ocean. We argue that we need to understand changes in diatom diversity, life cycle and plankton interactions in a warmer and more acidic ocean in much more detail to fully assess any changes in their contribution to the biological pump.

The role of diatom nanostructures in biasing diffusion to improve uptake in a patchy nutrient environment.

Directory of Open Access Journals (Sweden)

James G Mitchell

Full Text Available BACKGROUND: Diatoms are important single-celled autotrophs that dominate most lit aquatic environments and are distinguished by surficial frustules with intricate designs of unknown function. PRINCIPAL FINDINGS: We show that some frustule designs constrain diffusion to positively alter nutrient uptake. In nutrient gradients of 4 to 160 times over <5 cm, the screened-chambered morphology of Coscincodiscus sp. biases the nutrient diffusion towards the cell by at least 3.8 times the diffusion to the seawater. In contrast, the open-chambers of Thalassiosira eccentrica produce at least a 1.3 times diffusion advantage to the membrane over Coscincodiscus sp. when nutrients are homogeneous. SIGNIFICANCE: Diffusion constraint explains the success of particular diatom species at given times and the overall success of diatoms. The results help answer the unresolved question of how adjacent microplankton compete. Furthermore, diffusion constraint by supramembrane nanostructures to alter molecular diffusion suggests that microbes compete via supramembrane topology, a competitive mechanism not considered by the standard smooth-surface equations used for nutrient uptake nor in microbial ecology and cell physiology.

Epipsammic diatoms in streams influenced by urban pollution, São Carlos, SP, Brazil

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T. Bere

Full Text Available Epipsammic diatoms have important implications for ecosystem processes in lotic environments. Most of the studies on benthic diatoms concentrate on epilithic diatoms and very little is known about epipsammic diatoms. The objective of this study was to assess epipsammic diatom communities in streams in relation to environmental conditions. Epipsammic diatoms and water quality sampling was done at 7 sites during summer base flow period (2008. Forward stepwise multiple regression and canonical correspondence analysis (CCA were used to determine environmental gradients along which species vary with physical and chemical variables. A total of 112 diatom species distributed among 44 genera were recorded. Altitude and the process of eutrophication played a significant role in structuring diatom communities in the study region.

Codon adaptation and synonymous substitution rate in diatom plastid genes.

Science.gov (United States)

Morton, Brian R; Sorhannus, Ulf; Fox, Martin

2002-07-01

Diatom plastid genes are examined with respect to codon adaptation and rates of silent substitution (Ks). It is shown that diatom genes follow the same pattern of codon usage as other plastid genes studied previously. Highly expressed diatom genes display codon adaptation, or a bias toward specific major codons, and these major codons are the same as those in red algae, green algae, and land plants. It is also found that there is a strong correlation between Ks and variation in codon adaptation across diatom genes, providing the first evidence for such a relationship in the algae. It is argued that this finding supports the notion that the correlation arises from selective constraints, not from variation in mutation rate among genes. Finally, the diatom genes are examined with respect to variation in Ks among different synonymous groups. Diatom genes with strong codon adaptation do not show the same variation in synonymous substitution rate among codon groups as the flowering plant psbA gene which, previous studies have shown, has strong codon adaptation but unusually high rates of silent change in certain synonymous groups. The lack of a similar finding in diatoms supports the suggestion that the feature is unique to the flowering plant psbA due to recent relaxations in selective pressure in that lineage.

Quantification of diatoms in biofilms: Standardisation of methods

Digital Repository Service at National Institute of Oceanography (India)

Patil, J.S.; Anil, A.C.

of the difficulty in sampling and enumeration. Scraping or brushing are the traditional methods used for removal of diatoms from biofilms developed on solid substrata. The method of removal is the most critical step in enumerating the biofilm diatom community...

Aggregate Formation During the Viral Lysis of a Marine Diatom

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Yosuke Yamada

2018-05-01

Full Text Available Recent studies have suggested that the viral lysis of microbes not only facilitates the conversion of particulate organic matter into dissolved organic matter, but also promotes the formation of organic aggregates, which enhance the export of organic carbon from the surface ocean to the deep sea. However, experimental data supporting this proposition are limited. Here, we tested the hypothesis that the viral infection of marine diatoms enhances aggregate formation. We used a model system consisting of Chaetoceros tenuissimus, a bloom-forming diatom with an approximate cell size of 3–10 μm, and a DNA virus, CtenDNAV type II, which replicates in the nucleus of C. tenuissimus. The volume of large particles (50–400 μm in equivalent spherical diameters, determined from photographic images was measured over time (up to 15 days in the diatom-alone control and a virus-added diatom culture. We also determined the concentrations of Coomassie-stainable particles (CSP, proteinaceous particles and transparent exopolymeric particles (TEP, acid-polysaccharide-rich particles with colorimetric methods. The total volume of large particles was significantly higher (5–59 fold in the virus-added diatoms than in the diatom-alone control during the period in which the viral lysis of the diatoms proceeded. One class of large particles produced in the virus-added diatoms was flake-shaped. The flakes were tightly packed and dense, and sank rapidly, possibly playing an important role in the vertical delivery of materials from the surface to the deep sea. The bulk CSP concentrations tended to be higher in the virus-added diatoms than in the diatom-alone control, whereas the reverse was true for the TEP. These results suggest that proteinaceous polymers are involved in aggregate formation. Our data support the emerging notion that the viral lysis of microbes facilitates aggregate formation and the export of organic carbon in the ocean.

Architecture and material properties of diatom shells provide effective mechanical protection

Science.gov (United States)

Hamm, Christian E.; Merkel, Rudolf; Springer, Olaf; Jurkojc, Piotr; Maier, Christian; Prechtel, Kathrin; Smetacek, Victor

2003-02-01

Diatoms are the major contributors to phytoplankton blooms in lakes and in the sea and hence are central in aquatic ecosystems and the global carbon cycle. All free-living diatoms differ from other phytoplankton groups in having silicified cell walls in the form of two `shells' (the frustule) of manifold shape and intricate architecture whose function and role, if any, in contributing to the evolutionary success of diatoms is under debate. We explored the defence potential of the frustules as armour against predators by measuring their strength. Real and virtual loading tests (using calibrated glass microneedles and finite element analysis) were performed on centric and pennate diatom cells. Here we show that the frustules are remarkably strong by virtue of their architecture and the material properties of the diatom silica. We conclude that diatom frustules have evolved as mechanical protection for the cells because exceptional force is required to break them. The evolutionary arms race between diatoms and their specialized predators will have had considerable influence in structuring pelagic food webs and biogeochemical cycles.

Diatoms - nature materials with great potential for bioapplications

Directory of Open Access Journals (Sweden)

Medarević Đorđe P.

2016-01-01

Full Text Available Diatoms are widespread unicellular photosynthetic algae that produce unique highly ordered siliceous cell wall, called frustule. Micro- to nanoporous structure with high surface area that can be easily modified, high mechanical resistance, unique optical features (light focusing and luminescence and biocompatibility make diatom frustule as a suitable raw material for the development of devices such as bio- and gas sensors, microfluidic particle sorting devices, supercapacitors, batteries, solar cells, electroluminescent devices and drug delivery systems. Their wide availability in the form of fossil remains (diatomite or diatomaceous earth as well as easy cultivation in the artificial conditions further supports use of diatoms in many different fields of application. This review focused on the recent achievements in the diatom bioapplications such as drug delivery, biomolecules immobilization, bio- and gas sensing, since great progress was made in this field over the last several years.

Modified Ribose Receptor Response in Isolated Diatom Frustules

Energy Technology Data Exchange (ETDEWEB)

Fairbanks, Carly R.

2011-08-26

Diatoms are a distinctive group of microalgae with the unique ability to produce a highly-ordered biosilica matrix, known as the frustule. Diatoms hold significant potential in the biotechnology field as a silica scaffold for embedding proteins. In this study, we analyzed the funtionalization of biosilica with a receptor complex through genetic modification of the diatom, Thalassiosira pseudonana. Through the use of Foerster Resonance Energy Transfer (FRET), the receptor was shown to remain active in transformed frustules after the inner cellular contents were removed. In addition to protein functionality, growth conditions for T. pseudonana were optimized. Untransformed cultures receiving aeration grew more rapidly than stagnant untransformed cultures. Surprisingly, transformed cultures grew more quickly than untransformed cultures. This study demonstrates isolated diatom frustules provide an effective scaffold for embedded receptor complexes. Through this research, we provide the groundwork for the development of new biosensors for use in diagnostics and environmental remediation.

Comparing optical properties of different species of diatoms

DEFF Research Database (Denmark)

Maibohm, Christian; Friis, Søren Michael Mørk; Su, Y.

2015-01-01

species dependent with huge variety in size, shape, and micro- structure. We have experimentally investigated optical properties of frustules of several species of diatoms to further understand light harvesting properties together with commo n traits, effects and differences between the different...... analysis software. The software uses parameters which are extracted from experimental im ages as basis for simulation and allows us to extract the influence of the different elements of the frustule. The information could be used both for predicting optical properties of diatoms and by changing frustule...... parameters, maybe by altering growth conditions of the diatoms tailor their optical properties....

Molecular signatures in femtosecond laser-induced organic plasmas: comparison with nanosecond laser ablation.

Science.gov (United States)

Serrano, Jorge; Moros, Javier; Laserna, J Javier

2016-01-28

During the last few years, laser-induced breakdown spectroscopy (LIBS) has evolved significantly in the molecular sensing area through the optical monitoring of emissions from organic plasmas. Large efforts have been made to study the formation pathways of diatomic radicals as well as their connections with the bonding framework of molecular solids. Together with the structural and chemical-physical properties of molecules, laser ablation parameters seem to be closely tied to the observed spectral signatures. This research focuses on evaluating the impact of laser pulse duration on the production of diatomic species that populate plasmas of organic materials. Differences in relative intensities of spectral signatures from the plasmas of several organic molecules induced in femtosecond (fs) and nanosecond (ns) ablation regimes have been studied. Beyond the abundance and origin of diatomic radicals that seed the plasma, findings reveal the crucial role of the ablation regime in the breakage pattern of the molecule. The laser pulse duration dictates the fragments and atoms resulting from the vaporized molecules, promoting some formation routes at the expense of other paths. The larger amount of fragments formed by fs pulses advocates a direct release of native bonds and a subsequent seeding of the plasma with diatomic species. In contrast, in the ns ablation regime, the atomic recombinations and single displacement processes dominate the contribution to diatomic radicals, as long as atomization of molecules prevails over their progressive decomposition. Consequently, fs-LIBS better reflects correlations between strengths of emissions from diatomic species and molecular structure as compared to ns-LIBS. These new results entail a further step towards the specificity in the analysis of molecular solids by fs-LIBS.

Investigation of the silicon ion density during molecular beam epitaxy growth

Science.gov (United States)

Eifler, G.; Kasper, E.; Ashurov, Kh.; Morozov, S.

2002-05-01

Ions impinging on a surface during molecular beam epitaxy influence the growth and the properties of the growing layer, for example, suppression of dopant segregation and the generation of crystal defects. The silicon electron gun in the molecular beam epitaxy (MBE) equipment is used as a source for silicon ions. To use the effect of ion bombardment the mechanism of generation and distribution of ions was investigated. A monitoring system was developed and attached at the substrate position in the MBE growth chamber to measure the ion and electron densities towards the substrate. A negative voltage was applied to the substrate to modify the ion energy and density. Furthermore the current caused by charge carriers impinging on the substrate was measured and compared with the results of the monitoring system. The electron and ion densities were measured by varying the emission current of the e-gun achieving silicon growth rates between 0.07 and 0.45 nm/s and by changing the voltage applied to the substrate between 0 to -1000 V. The dependencies of ion and electron densities were shown and discussed within the framework of a simple model. The charged carrier densities measured with the monitoring system enable to separate the ion part of the substrate current and show its correlation to the generation rate. Comparing the ion density on the whole substrate and in the center gives a hint to the ion beam focusing effect. The maximum ion and electron current densities obtained were 0.40 and 0.61 μA/cm2, respectively.

A new cell primo-culture method for freshwater benthic diatom communities

OpenAIRE

Debenest, Timothée; Silvestre, Jérôme; Coste, Michel; Delmas, François; Pinelli, Eric

2009-01-01

A new cell primo-culture method was developed for the benthic diatom community isolated from biofilm sampled in rivers. The approach comprised three steps: (1) scraping biofilm from river pebbles, (2) diatom isolation from biofilm, and (3) diatom community culture. With a view to designing a method able to stimulate the growth of diatoms, to limit the development of other microorganisms, and to maintain in culture a community similar to the original natural one, different factors were test...

Diatoms: a fossil fuel of the future.

Science.gov (United States)

Levitan, Orly; Dinamarca, Jorge; Hochman, Gal; Falkowski, Paul G

2014-03-01

Long-term global climate change, caused by burning petroleum and other fossil fuels, has motivated an urgent need to develop renewable, carbon-neutral, economically viable alternatives to displace petroleum using existing infrastructure. Algal feedstocks are promising candidate replacements as a 'drop-in' fuel. Here, we focus on a specific algal taxon, diatoms, to become the fossil fuel of the future. We summarize past attempts to obtain suitable diatom strains, propose future directions for their genetic manipulation, and offer biotechnological pathways to improve yield. We calculate that the yields obtained by using diatoms as a production platform are theoretically sufficient to satisfy the total oil consumption of the US, using between 3 and 5% of its land area. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effect of the Silica Content of Diatoms on Protozoan Grazing

Directory of Open Access Journals (Sweden)

Shuwen Zhang

2017-06-01

Full Text Available This study examined the effect that silica content in diatom cells has on the behavior of protists. The diatoms Thalassiosira weissflogii and T. pseudonana were cultured in high or low light conditions to achieve low and high silica contents, respectively. These cells were then fed to a heterotrophic dinoflagellate Noctiluca scintillans and a ciliate Euplotes sp. in single and mixed diet experiments. Our results showed that in general, N. scintillans and Euplotes sp. both preferentially ingested the diatoms with a low silica content rather than those with a high silica content. However, Euplotes sp. seemed to be less influenced by the silica content than was N. scintillans. In the latter case, the clearance and ingestion rate of the low silica diatoms were significantly higher, both in the short (6-h and long (1-d duration grazing experiments. Our results also showed that N. scintillans required more time to digest the high silica-containing cells. As the high silica diatoms are harder to digest, this might explain why N. scintillans exhibits a strong preference for the low silica prey. Thus, the presence of high silica diatoms might limit the ability of the dinoflagellate to feed. Our findings suggest that the silica content of diatoms affects their palatability and digestibility and, consequently, the grazing activity and selectivity of protozoan grazers.

Diatom-induced silicon isotopic fractionation in Antarctic sea ice

Science.gov (United States)

Francois, F.; Damien, C.; Jean-Louis, T.; Anthony, W.; Luc, A.

2006-12-01

We measured silicon-isotopic composition of dissolved silicon and biogenic silica collected by sequential melting from spring 2003 Antarctic pack ice (Australian sector). Sea ice is a key ecosystem in the Southern Ocean and its melting in spring has been often thought to have a seeding effect for the surface waters, triggering blooms in the mixed layer. This work is the first investigation of the silicon isotopes' proxy in sea ice and allows to estimate the activity of sea-ice diatoms in the different brine structures and the influence of sea- ice diatoms on the spring ice edge blooms. The relative use of the dissolved silicon pool by sea-ice diatoms is usually assessed by calculating nutrient:salinity ratios in the brines. However such an approach is biased by difficulties in evaluating the initial nutrient concentrations in the different brines structures, and by the impossibility to account for late sporadic nutrient replenishments. The silicon-isotopic composition of biogenic silica is a convenient alternative since it integrates an average Si utilization on all generations of diatoms. Measurements were performed on a MC-ICP-MS, in dry plasma mode using external Mg doping. Results are expressed as delta29Si relative to the NBS28 standard. From three sea ice cores with contrasted physico-chemical characteristics, we report significant isotopic fractionations linked to the diatoms activity, with distinct silicon biogeochemical dynamics between different brine structure. The diatoms in snow ice and in brine pockets of frazil or congelation ice have the most positive silicon-isotopic composition (+0.53 to +0.86 p.mil), indicating that they grow in a closed system and use a significant part of the small dissolved silicon pool. In the brine channels and skeletal layer, diatoms display a relatively less positive Si-isotopic composition (+0.41 to +0.70 p.mil), although it is still heavier compared to equilibrium fractionation (+0.38 p.mil). This suggests that they have

Quantum entanglement and the dissociation process of diatomic molecules

Energy Technology Data Exchange (ETDEWEB)

Esquivel, Rodolfo O; Molina-Espiritu, Moyocoyani [Departamento de Quimica, Universidad Autonoma Metropolitana, 09340-Mexico DF (Mexico); Flores-Gallegos, Nelson [Unidad Profesional Interdisciplinaria de IngenierIa, Campus Guanajuato del Instituto Politecnico Nacional, 36275-Guanajuato (Mexico); Plastino, A R; Angulo, Juan Carlos; Dehesa, Jesus S [Instituto Carlos I de Fisica Teorica y Computacional, and Departamento de Fisica Atomica, Molecular y Nuclear, Universidad de Granada, 18071-Granada (Spain); Antolin, Juan, E-mail: esquivel@xanum.uam.mx, E-mail: arplastino@ugr.es [Departamento de Fisica Aplicada, EUITIZ, Universidad de Zaragoza, 50018-Zaragoza (Spain)

2011-09-14

In this work, we investigate quantum entanglement-related aspects of the dissociation process of some selected, representative homo- and heteronuclear diatomic molecules. This study is based upon high-quality ab initio calculations of the (correlated) molecular wavefunctions involved in the dissociation processes. The values of the electronic entanglement characterizing the system in the limit cases corresponding to (i) the united-atom representation and (ii) the asymptotic region when atoms dissociate are discussed in detail. It is also shown that the behaviour of the electronic entanglement as a function of the reaction coordinate R exhibits remarkable correspondences with the phenomenological description of the physically meaningful regimes comprising the processes under study. In particular, the extrema of the total energies and the electronic entanglement are shown to be associated with the main physical changes experienced by the molecular spatial electronic density, such as charge depletion and accumulation or bond cleavage regions. These structural changes are characterized by several selected descriptors of the density, such as the Laplacian of the electronic molecular distributions (LAP), the molecular electrostatic potential (MEP) and the atomic electric potentials fitted to the MEP.

Response of the marine diatom Thalassiosira weissflogii to iron stress

International Nuclear Information System (INIS)

Harrison, G.I.; Morel, F.M.M.

1986-01-01

The coastal diatom Thalassiosira weissflogii responds to iron limitation with decreasing growth rate, decreasing quotas of cellular iron, and increasing rates of maximum short term uptake. Growth response to steady iron limitation can be modeled according to the equations of Droop and Monod. The cellular iron quota varies from about 2 to 25 x 10 -1 mol iron per liter-cell with increasing iron; the half-saturation constant for growth, Kμ, is 1.1 x 10 -21 M (free ferric ion). In contrast, the half-saturation constant for 59 I iron uptake, K/sub rho/ is about 3 x 10 -19 M; the maximum iron uptake rate (rho/sub max/) is increased several-fold under iron limitation, resulting in a potential short term uptake rate that is a few hundred times the steady state rate. At a fixed concentration of free manganese ion, the cellular manganese quota is increased several-fold in iron-limited cultures compared to iron-sufficient cultures

Automated Diatom Classification (Part A: Handcrafted Feature Approaches

Directory of Open Access Journals (Sweden)

Gloria Bueno

2017-07-01

Full Text Available This paper deals with automatic taxa identification based on machine learning methods. The aim is therefore to automatically classify diatoms, in terms of pattern recognition terminology. Diatoms are a kind of algae microorganism with high biodiversity at the species level, which are useful for water quality assessment. The most relevant features for diatom description and classification have been selected using an extensive dataset of 80 taxa with a minimum of 100 samples/taxon augmented to 300 samples/taxon. In addition to published morphological, statistical and textural descriptors, a new textural descriptor, Local Binary Patterns (LBP, to characterize the diatom’s valves, and a log Gabor implementation not tested before for this purpose are introduced in this paper. Results show an overall accuracy of 98.11% using bagging decision trees and combinations of descriptors. Finally, some phycological features of diatoms that are still difficult to integrate in computer systems are discussed for future work.

What if the Diatoms of the Deep Chlorophyll Maximum Can Ascend?

Science.gov (United States)

Villareal, T. A.

2016-02-01

Buoyancy regulation is an integral part of diatom ecology via its role in sinking rates and is fundamental to understanding their distribution and abundance. Numerous studies have documented the effects of size and nutrition on sinking rates. Many pelagic diatoms have low intrinsic sinking rates when healthy and nutrient-replete (deep chlorophyll maximum. The potential for ascending behavior adds an additional layer of complexity by allowing both active depth regulation similar to that observed in flagellated taxa and upward transport by some fraction of deep euphotic zone diatom blooms supported by nutrient injection. In this talk, I review the data documenting positive buoyancy in small diatoms, offer direct visual evidence of ascending behavior in common diatoms typical of both oceanic and coastal zones, and note the characteristics of sinking rate distributions within a single species. Buoyancy control leads to bidirectional movement at similar rates across a wide size spectrum of diatoms although the frequency of ascending behavior may be only a small portion of the individual species' abundance. While much remains to be learned, the paradigm of unidirectional downward movement by diatoms is both inaccurate and an oversimplification.

TRIGLYCERIDE COMPOSITION OF SIXTEEN STRAINS OF MARINE DIATOM

Directory of Open Access Journals (Sweden)

Lily M.G. Panggabean

2013-07-01

Full Text Available Trigliceride or triacylglicerol (TAG composition in crude oil of sixteen strain of marine diatom has been detected by spectra analyses on an Electrospray - Ion Trap – Mass Spectrometry (ESI-IT-MS HCT Bruker-Daltonic GmbH instrument with AgNO3 used as coordination ionization agent. Biomass samples of each microalga strain were taken from early and late stationary cultures in f/2 enriched seawater and algal oils were extracted according to Bligh and Dyer. Results from spectra analysis showed that P-Pt-P (C16:0-C16:1-C16:0 were distinguished in TAG from diatom strains Chaetoceros sp.1, Chaetoceros sp.2, Thalasiossira sp.1, Thalasiossira sp.2, Thalasiossira sp.3, Navicula sp. 1, Navicula sp. 2, Navicula sp. 3, Navicula sp. 4, Nitzschia sp. 2 and Amphora sp. In contrast, TAGs in Melosira sp. included P-P-P (C16:0-C16:0-C16:0 and P-P-O (C16:0-C16:0-C18:1 were identified. TAGs from Chaetoceros sp. were the most varies among samples, i.e. P-Pt-P (C16:0-C16:1-C16:0, A-P-M (C20:4-C16:0-C14:0, P-Pt-Lt (C16:0-C16:1-C18:3, P-Pt-A (C16:0-C16:1-C20:4, D-P-P (C22:6-C16:0-C16:0, A-Ln-P (C20:4-C18:2-C16:0. Various TAGs were also detected in Nitzschia sp.2, i.e. P-Pt-M (C16:0-C16:1-C14:0, P-Pt-P (C16:0-C16:1-C16:0, P-Pt-S (C16:0-C16:1-C18:0, P-Pt-A (C16:0-C16:1-C20:4. TAGs composition in Skeletonema strains that similar to those in Nitzschia sp.1 has longer carbon, i.e. P-P-O (C16:0-C16:0-C18:1, P-O-O (C16:0-C18:1-C18:1 and O-O-O (C18:1-C18:1-C18:1. TAGs with longer carbon chain and more double bond including highly unsaturated fatty acid C20:4 were increased with culture age in diatoms Chaetoceros sp.1, Chaetoceros sp.2, Thalasiossira sp.2, Navicula sp.1 and Nitzschia sp. 2.Keywords: diatom, TAG, ESI-IT-MS, f/2, early and late stationary

Diatom-based water quality monitoring in southern Africa ...

African Journals Online (AJOL)

The purpose of this review is to summarise the challenges and future prospects associated with biological water quality monitoring using diatoms with special focus on southern Africa. Much work still needs to be carried out on diatom tolerances, ecological preferences and ecophysiology. It is recommended that past ...

Molecular dynamics studies of the ion beam induced crystallization in silicon

International Nuclear Information System (INIS)

Marques, L.A.; Caturla, M.J.; Huang, H.

1995-01-01

We have studied the ion bombardment induced amorphous-to-crystal transition in silicon using molecular dynamics techniques. The growth of small crystal seeds embedded in the amorphous phase has been monitored for several temperatures in order to get information on the effect of the thermal temperature increase introduced by the incoming ion. The role of ion-induced defects on the growth has been also studied

Ion channels: molecular targets of neuroactive insecticides.

Science.gov (United States)

Raymond-Delpech, Valérie; Matsuda, Kazuhiko; Sattelle, Benedict M; Rauh, James J; Sattelle, David B

2005-11-01

Many of the insecticides in current use act on molecular targets in the insect nervous system. Recently, our understanding of these targets has improved as a result of the complete sequencing of an insect genome, i.e., Drosophila melanogaster. Here we examine the recent work, drawing on genetics, genomics and physiology, which has provided evidence that specific receptors and ion channels are targeted by distinct chemical classes of insect control agents. The examples discussed include, sodium channels (pyrethroids, p,p'-dichlorodiphenyl-trichloroethane (DDT), dihydropyrazoles and oxadiazines); nicotinic acetylcholine receptors (cartap, spinosad, imidacloprid and related nitromethylenes/nitroguanidines); gamma-aminobutyric acid (GABA) receptors (cyclodienes, gamma-BHC and fipronil) and L-glutamate receptors (avermectins). Finally, we have examined the molecular basis of resistance to these molecules, which in some cases involves mutations in the molecular target, and we also consider the future impact of molecular genetic technologies in our understanding of the actions of neuroactive insecticides.

Rotational Laser Cooling of Vibrationally and Translationally Cold Molecular Ions

DEFF Research Database (Denmark)

Drewsen, Michael

2011-01-01

[7,8,9]. Furthermore, in order to learn more about the chemistry in interstellar clouds, astrochemists can benefit greatly from direct measurements on cold reactions in laboratories [9]. Working with MgH+ molecular ions in a linear Paul trap, we routinely cool their translational degree of freedom...... by sympathetic cooling with Doppler laser cooled Mg+ ions. Giving the time for the molecules to equilibrate internally to the room temperature blackbody radiation, the vibrational degree of freedom will freeze out, leaving only the rotational degree of freedom to be cooled. We report here on the implementation...... results imply that, through this technique, cold molecular-ion experiments can now be carried out at cryogenic temperatures in room-temperature set-ups. References [1] Koelemeij, J. C. J., Roth, B., Wicht, A., Ernsting, I. and Schiller, S., Phys. Rev. Lett. 98, 173002 (2007). [2] Hudson, J. J., Sauer, B...

In vivo exposure to northern diatoms arrests sea urchin embryonic development.

Science.gov (United States)

Gudimova, Elena; Eilertsen, Hans C; Jørgensen, Trond Ø; Hansen, Espen

2016-01-01

There are numerous reports indicating that marine diatoms may act harmful to early developmental stages of invertebrates. It is believed that the compounds responsible for these detrimental effects are oxylipins resulting from oxidized polyunsaturated fatty acids, and that they may function as grazing deterrents. Most studies reporting these effects have exposed test organisms to diatom extracts or purified toxins, but data from in vivo exposure to intact diatoms are scarce. We have conducted sea urchin egg incubation and plutei feeding experiments to test if intact diatom cells affected sea urchin embryo development and survival. This was done by exposing the common northern sea urchins Strongylocentrotus droebachiensis and Echinus acutus to northern strains of the diatoms Chaetoceros socialis, Skeletonema marinoi, Chaetoceros furcellatus, Attheya longicornis, Thalassiosira gravida and Porosira glacialis. The intact diatom cell suspensions were found to inhibit sea urchin egg hatching and embryogenesis. S. marinoi was the most potent one as it caused acute mortality in S. droebachiensis eggs after only four hours exposure to high (50 μg/L Chla) diatom concentrations, as well as 24 h exposure to normal (20 μg/L Chla) and high diatom concentrations. The second most potent species was T. gravida that caused acute mortality after 24 h exposure to both diatom concentrations. A. longicornis was the least harmful of the diatom species in terms of embryo development arrestment, and it was the species that was most actively ingested by S. droebachiensis plutei. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

The genome of the diatom Thalassiosira pseudonana: Ecology,evolution, and metabolism

Energy Technology Data Exchange (ETDEWEB)

Ambrust, E.V.; Berges, J.; Bowler, C.; Green, B.; Martinez, D.; Putnam, N.; Zhou, S.; Allen, A.; Apt, K.; Bechner, M.; Brzezinski, M.; Chaal, B.; Chiovitti, A.; Davis, A.; Goodstein, D.; Hadi, M.; Hellsten,U.; Hildebrand, M.; Jenkins, B.; Jurka, J.; Kapitonov, V.; Kroger, N.; Lau, W.; Lane, T.; Larimer, F.; Lippmeier, J.; Lucas, S.; Medina, M.; Montsant, A.; Obornik, M.; Parker, M. Schnitzler; Palenik, B.; Pazour,G.; Richardson, P.; Rynearson, T.; Saito, M.; Schwartz, D.; Thamatrakoln,K.; Valentin, K.; Vardi, A.; Wilkerson, F.; Rokhsar, D.; Vardi, A.; Wilkerson, F.P.; Rokhsar, D.S.

2004-09-01

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for {approx}20% of global carbon fixation. We report the 34 Mbp draft nuclear genome of the marine diatom, Thalassiosira pseudonana and its 129 Kbp plastid and 44 Kbp mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, utilization of a range of nitrogenous compounds and a complete urea cycle, all attributes that allow diatoms to prosper in the marine environment. Diatoms are unicellular, photosynthetic, eukaryotic algae found throughout the world's oceans and freshwater systems. They form the base of short, energetically-efficient food webs that support large-scale coastal fisheries. Photosynthesis by marine diatoms generates as much as 40% of the 45-50 billion tonnes of organic carbon produced each year in the sea (1), and their role in global carbon cycling is predicted to be comparable to that of all terrestrial rainforests combined (2, 3). Over geological time, diatoms may have influenced global climate by changing the flux of atmospheric carbon dioxide into the oceans (4). A defining feature of diatoms is their ornately patterned silicified cell wall or frustule, which displays species-specific nano-structures of such fine detail that diatoms have long been used to test the resolution of optical microscopes. Recent attention has focused on biosynthesis of these nano-structures as a paradigm for future silica nanotechnology (5). The long history (over 180 million years) and dominance of diatoms in the oceans is reflected by their contributions to vast deposits of diatomite, most cherts and a significant fraction of current petroleum reserves (6). As photosynthetic heterokonts, diatoms reflect a fundamentally

Transmission of fast molecular ions through thin foils

International Nuclear Information System (INIS)

Pietsch, W.J.; Gemmell, D.S.; Cooney, P.J.; Kanter, E.P.; Kurath, D.; Ratkowski, A.J.; Vager, Z.; Zabransky, B.J.

1979-01-01

New results on the transmission of fast molecular ions through thin foils are presented and a mechanism for the transmission process is proposed. The main feature of the postulated mechanism is that a finite fraction of the incident molecular beam does not undergo a strong Coulomb explosion while traversing the foil. Because the emerging fragments are at large internuclear separations, there is an enhanced probability for the formation of bound, long-range, excited electronic states following electron capture at the rear surface of the target

Specificity of lipoxygenase pathways supports species delineation in the marine diatom genus Pseudo-nitzschia.

Directory of Open Access Journals (Sweden)

Nadia Lamari

Full Text Available Oxylipins are low-molecular weight secondary metabolites derived from the incorporation of oxygen into the carbon chains of polyunsaturated fatty acids (PUFAs. Oxylipins are produced in many prokaryotic and eukaryotic lineages where they are involved in a broad spectrum of actions spanning from stress and defense responses, regulation of growth and development, signaling, and innate immunity. We explored the diversity in oxylipin patterns in the marine planktonic diatom Pseudo-nitzschia. This genus includes several species only distinguishable with the aid of molecular markers. Oxylipin profiles of cultured strains were obtained by reverse phase column on a liquid chromatograph equipped with UV photodiode detector and q-ToF mass spectrometer. Lipoxygenase compounds were mapped on phylogenies of the genus Pseudo-nitzschia inferred from the nuclear encoded hyper-variable region of the LSU rDNA and the plastid encoded rbcL. Results showed that the genus Pseudo-nitzschia exhibits a rich and varied lipoxygenase metabolism of eicosapentaenoic acid (EPA, with a high level of specificity for oxylipin markers that generally corroborated the genotypic delineation, even among genetically closely related cryptic species. These results suggest that oxylipin profiles constitute additional identification tools for Pseudo-nitzschia species providing a functional support to species delineation obtained with molecular markers and morphological traits. The exploration of the diversity, patterns and plasticity of oxylipin production across diatom species and genera will also provide insights on the ecological functions of these secondary metabolites and on the selective pressures driving their diversification.

The import and function of diatom and plant frataxins in the mitochondrion of Trypanosoma brucei

Czech Academy of Sciences Publication Activity Database

Long, Shaojun; Vávrová, Zuzana; Lukeš, Julius

2008-01-01

Roč. 162, č. 1 (2008), s. 100-104 ISSN 0166-6851 R&D Projects: GA AV ČR IAA500960705; GA MŠk LC07032; GA MŠk 2B06129; GA ČR GA204/06/1558 Institutional research plan: CEZ:AV0Z60220518 Keywords : frataxin * mitochondrion * Trypanosoma * diatom * evolutionary conservativeness * import Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.951, year: 2008

Soliton solutions in a diatomic lattice system

International Nuclear Information System (INIS)

Yajima, Nobuo; Satsuma, Junkichi.

1979-04-01

A continuum limit is considered for a diatomic lattice system with a cubic nonlinearity. A long wave equation describing the interaction of acoustic and optical modes is obtained. It reduces, in certain approximations, to equations having coupled wave solutions. The solutions exhibit trapping of an optical mode by an acoustic soliton. The form of the trapped optical wave depends on the mass ratio of adjacent particles in the diatomic lattice. (author)

The rotational temperature of polar molecular ions in Coulomb crystals

International Nuclear Information System (INIS)

Bertelsen, Anders; Joergensen, Solvejg; Drewsen, Michael

2006-01-01

With MgH + ions as a test case, we investigate to what extent the rotational motion of smaller polar molecular ions sympathetically cooled into Coulomb crystals in linear Paul traps couples to the translational motions of the ion ensemble. By comparing the results obtained from rotational resonance-enhanced multiphoton photo-dissociation experiments with data from theoretical simulations, we conclude that the effective rotational temperature exceeds the translational temperature (<100 mK) by more than two orders of magnitude, indicating a very weak coupling. (letter to the editor)

Trapped ion simulation of molecular spectrum

Science.gov (United States)

Shen, Yangchao; Lu, Yao; Zhang, Kuan; Zhang, Shuaining; Huh, Joonsuk; Kim, Kihwan

2016-05-01

Boson sampling had been suggested as a classically intractable and quantum mechanically manageable problem via computational complexity theory arguments. Recently, Huh and co-workers proposed theoretically a modified version of boson sampling, which is designed to simulate a molecular problem, as a practical application. Here, we report the experimental implementation of the theoretical proposal with a trapped ion system. As a first demonstration, we perform the quantum simulation of molecular vibronic profile of SO2, which incorporates squeezing, rotation and coherent displacements operations, and the collective projection measurement on phonon modes. This work was supported by the National Basic Research Program of China 11CBA00300, 2011CBA00301, National Natural Science Foundation of China 11374178, 11574002. Basic Science Research Program of Korea NRF-2015R1A6A3A04059773.

Study of the interaction of potassium ion channel protein with micelle by molecular dynamics simulation

Science.gov (United States)

Shantappa, Anil; Talukdar, Keka

2018-04-01

Ion channels are proteins forming pore inside the body of all living organisms. This potassium ion channel known as KcsA channel and it is found in the each cell and nervous system. Flow of various ions is regulated by the function of the ion channels. The nerve ion channel protein with protein data bank entry 1BL8, which is basically an ion channel protein in Streptomyces Lividans and which is taken up to form micelle-protein system and the system is analyzed by using molecular dynamics simulation. Firstly, ion channel pore is engineered by CHARMM potential and then Micelle-protein system is subjected to molecular dynamics simulation. For some specific micelle concentration, the protein unfolding is observed.

Molecular Mechanisms of Ion-Specific Effects on Proteins

Czech Academy of Sciences Publication Activity Database

Rembert, K. B.; Paterová, Jana; Heyda, Jan; Hilty, Ch.; Jungwirth, Pavel; Cremer, P. S.

2012-01-01

Roč. 134, č. 24 (2012), s. 10039-10046 ISSN 0002-7863 R&D Projects: GA ČR GA203/08/0114 Institutional research plan: CEZ:AV0Z40550506 Keywords : ions * proteins * molecular dynamics * NMR Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 10.677, year: 2012

Chemical effects induced by ion implantation in molecular solids

International Nuclear Information System (INIS)

Foti, G.; Calcagno, L.; Puglisi, O.

1983-01-01

Ion implantation in molecular solids as ice, frozen noble gases, benzene and polymers produces a large amount of new molecules compared to the starting materials. Mass and energy analysis of ejected molecules together with the erosion yield, are discussed for several ion-target combinations at low temperature. The observed phenomena are analyzed in terms of deposited ennergy in electronic and nuclear collisions, for incoming beams, as helium or argon, in the range 10-2000 keV. (orig.)

Review--Interactions between diatoms and stainless steel: focus on biofouling and biocorrosion.

Science.gov (United States)

Landoulsi, J; Cooksey, K E; Dupres, V

2011-11-01

There is a considerable body of information regarding bacterially enhanced corrosion, however, this review focuses on diatoms (unicellular algae) whose contribution to biocorrosion is less well studied. The reasons why diatoms have been neglected in studies of biocorrosion in natural waters are discussed and the question whether diatoms should be considered as inert with respect of electrochemical processes is considered. A particular focus is given to the case of stainless steels (SS), which are widely used in variety of applications in natural waters. Basic information on the cell biology of diatoms is included in the review, particularly with respect to their ability to 'sense' and adhere to surfaces. Investigations at the nanoscale are reviewed as these studies provide information about the behavior of cells at interfaces. Recent advances include the use of atomic force microscopy (AFM), although only a few studies have been applied to diatoms. Regarding the electrochemical behavior of SS, the mechanisms by which diatoms influence the potential ennoblement process is discussed. Such studies reveal the association of diatoms, in addition to bacteria, with biocorrosion processes.

Molecular analysis of carbon ion-induced mutations in Arabidopsis thaliana

International Nuclear Information System (INIS)

Shikazono, Naoya; Tanaka, Atsushi; Watanabe, Hiroshi; Tano, Shigemitsu; Yokota, Yukihiko

1998-01-01

In order to elucidate the characteristics of the mutations induced by ion particles at the molecular level in plants, mutated loci in carbon ion-induced mutants of Arabidopsis were investigated by PCR and Southern blot analyses. In the present study, two lines of gl1 mutant and two lines of tt4 mutant were isolated after carbon ion-irradiation. Out of four mutants, one had a deletion, other two contained rearrangements, and one had a point-like mutation. From the present result, it was suggested that ion particles induced different kinds of alterations of the DNA and therefore they could produce various types of mutant alleles in plants. (author)

Isolation of diatom Navicula cryptocephala and characterization of ...

African Journals Online (AJOL)

sjce

synthesis to the storage of neutral lipids (Qiang et al.,. 2008). Diatoms were shown ... chemical analysis of the oil inside diatom oil droplets, a method for separating ... 120°C for 20 min. 0.1 mg.L. −1. Thiamine, 0.5 μg.L. −1. Biotin and 0.5 μg.L−1.

Electron collisions and internal excitation in stored molecular ion beams

International Nuclear Information System (INIS)

Buhr, H.

2006-01-01

In storage ring experiments the role, which the initial internal excitation of a molecular ion can play in electron collisions, and the effect of these collisions on the internal excitation are investigated. Dissociative recombination (DR) and inelastic and super-elastic collisions are studied in the system of He + 2 . The DR rate coefficient at low energies depends strongly on the initial vibrational excitation in this system. Therefore changes in the DR rate coefficient are a very sensitive probe for changes in the vibrational excitation in He + 2 , which is used to investigate the effects of collisions with electrons and residual gas species. The low-energy DR of HD + is rich with resonances from the indirect DR process, when certain initial rotational levels in the molecular ion are coupled to levels in neutral Rydberg states lying below the ion state. Using new procedures for high-resolution electron-ion collision spectroscopy developed here, these resonances in the DR cross section can be measured with high energy sensitivity. This allows a detailed comparison with results of a MQDT calculation in an effort to assign some or all of the resonances to certain intermediate Rydberg levels. (orig.)

Electron collisions and internal excitation in stored molecular ion beams

Energy Technology Data Exchange (ETDEWEB)

Buhr, H.

2006-07-26

In storage ring experiments the role, which the initial internal excitation of a molecular ion can play in electron collisions, and the effect of these collisions on the internal excitation are investigated. Dissociative recombination (DR) and inelastic and super-elastic collisions are studied in the system of He{sup +}{sub 2}. The DR rate coefficient at low energies depends strongly on the initial vibrational excitation in this system. Therefore changes in the DR rate coefficient are a very sensitive probe for changes in the vibrational excitation in He{sup +}{sub 2}, which is used to investigate the effects of collisions with electrons and residual gas species. The low-energy DR of HD{sup +} is rich with resonances from the indirect DR process, when certain initial rotational levels in the molecular ion are coupled to levels in neutral Rydberg states lying below the ion state. Using new procedures for high-resolution electron-ion collision spectroscopy developed here, these resonances in the DR cross section can be measured with high energy sensitivity. This allows a detailed comparison with results of a MQDT calculation in an effort to assign some or all of the resonances to certain intermediate Rydberg levels. (orig.)

A Zeeman slower for diatomic molecules

Science.gov (United States)

Petzold, M.; Kaebert, P.; Gersema, P.; Siercke, M.; Ospelkaus, S.

2018-04-01

We present a novel slowing scheme for beams of laser-coolable diatomic molecules reminiscent of Zeeman slowing of atomic beams. The scheme results in efficient compression of the one-dimensional velocity distribution to velocities trappable by magnetic or magneto-optical traps. We experimentally demonstrate our method in an atomic testbed and show an enhancement of flux below v = 35 m s‑1 by a factor of ≈20 compared to white light slowing. 3D Monte Carlo simulations performed to model the experiment show excellent agreement. We apply the same simulations to the prototype molecule 88Sr19F and expect 15% of the initial flux to be continuously compressed in a narrow velocity window at around 10 m s‑1. This is the first experimentally shown continuous and dissipative slowing technique in molecule-like level structures, promising to provide the missing link for the preparation of large ultracold molecular ensembles.

Marennine, Promising Blue Pigments from a Widespread Haslea Diatom Species Complex

Directory of Open Access Journals (Sweden)

Romain Gastineau

2014-05-01

Full Text Available In diatoms, the main photosynthetic pigments are chlorophylls a and c, fucoxanthin, diadinoxanthin and diatoxanthin. The marine pennate diatom Haslea ostrearia has long been known for producing, in addition to these generic pigments, a water-soluble blue pigment, marennine. This pigment, responsible for the greening of oysters in western France, presents different biological activities: allelopathic, antioxidant, antibacterial, antiviral, and growth-inhibiting. A method to extract and purify marennine has been developed, but its chemical structure could hitherto not be resolved. For decades, H. ostrearia was the only organism known to produce marennine, and can be found worldwide. Our knowledge about H. ostrearia-like diatom biodiversity has recently been extended with the discovery of several new species of blue diatoms, the recently described H. karadagensis, H. silbo sp. inedit. and H. provincialis sp. inedit. These blue diatoms produce different marennine-like pigments, which belong to the same chemical family and present similar biological activities. Aside from being a potential source of natural blue pigments, H. ostrearia-like diatoms thus present a commercial potential for aquaculture, cosmetics, food and health industries.

Diatom diet selectivity by early post-larval abalone Haliotis diversicolor supertexta under hatchery conditions

Science.gov (United States)

Zhang, Yuyu; Gao, Yahui; Liang, Junrong; Chen, Changping; Zhao, Donghai; Li, Xuesong; Li, Yang; Wu, Wenzhong

2010-11-01

Benthic diatoms constitute the primary diet of abalone during their early stages of development. To evaluate the dietary preferences of early post-larval abalone, Haliotis diversicolor supertexta, we analyzed the gut contents of post-larvae that settled on diatom films. We compared the abundance and species diversity of diatom assemblages in the gut to those of the epiphytic diatom assemblages on the attachment films, and identified 40 benthic diatom species in the gut contents of post-larvae 12 to 24 d after settlement. The most abundant taxa in the gut contents were Navicula spp., Amphora copulate, and Amphora coffeaeformis. Navicula spp. accounted for 64.0% of the cell density. In the attachment films, we identified 110 diatom species belonging to 38 genera. Pennate diatoms were the dominant members including the species Amphiprora alata, Cocconeis placentula var. euglypta, Cylindrotheca closterium, Navicula sp. 2, and A. coffeaeformis. Nano-diatoms (abalone seed. The difference of the composition and abundance of diatoms between in the guts and on the biofilms suggests that early post-larval grazing was selective. An early post-larval abalone preferred nano-diatoms and the genera Navicula and Amphora during the month after settlement.

A controllable molecular sieve for Na+ and K+ ions.

Science.gov (United States)

Gong, Xiaojing; Li, Jichen; Xu, Ke; Wang, Jianfeng; Yang, Hui

2010-02-17

The selective rate of specific ion transport across nanoporous material is critical to biological and nanofluidic systems. Molecular sieves for ions can be achieved by steric and electrical effects. However, the radii of Na(+) and K(+) are quite similar; they both carry a positive charge, making them difficult to separate. Biological ionic channels contain precisely arranged arrays of amino acids that can efficiently recognize and guide the passage of K(+) or Na(+) across the cell membrane. However, the design of inorganic channels with novel recognition mechanisms that control the ionic selectivity remains a challenge. We present here a design for a controllable ion-selective nanopore (molecular sieve) based on a single-walled carbon nanotube with specially arranged carbonyl oxygen atoms modified inside the nanopore, which was inspired by the structure of potassium channels in membrane spanning proteins (e.g., KcsA). Our molecular dynamics simulations show that the remarkable selectivity is attributed to the hydration structure of Na(+) or K(+) confined in the nanochannels, which can be precisely tuned by different patterns of the carbonyl oxygen atoms. The results also suggest that a confined environment plays a dominant role in the selectivity process. These studies provide a better understanding of the mechanism of ionic selectivity in the KcsA channel and possible technical applications in nanotechnology and biotechnology, including serving as a laboratory-in-nanotube for special chemical interactions and as a high-efficiency nanodevice for purification or desalination of sea and brackish water.

Inelastic surface collisions and the desorption of massive molecular ions

Energy Technology Data Exchange (ETDEWEB)

Macfarlane, R D [Texas A and M Univ., College Station (USA). Dept. of Chemistry

1983-01-01

The interaction of high energy ions in the region of electronic stopping (1 MeV u/sup -1/) stimulates the desorption of massive molecular ions of biomolecules such as insulin. The experimental details of the measurements are given with some examples of application for analytical mass spectrometry. Studies on the role of the incident ion (accelerator beam experiments) are reviewed as well as the contribution of the matrix to the desorption-ionization process. How the electronic relaxation process couples to desorption-ionization is a central question in understanding the overall mechanism of the process.

Solvation of ions in the gas-phase: a molecular dynamics simulation

Science.gov (United States)

Cabarcos, Orlando M.; Lisy, James M.

1996-07-01

Molecular dynamics simulations have been performed on the collision between a cesium ion and a cluster of twenty methanol molecules. This process, generating a solvated ion, was studied over a range (1 to 25 eV) of eight collision energies. Preliminary analysis of this gas phase solvation has included the distribution of final ion cluster sizes, fragmentation patterns, solvation timescales and energetics. Two distinct patterns have emerged: a ballistic penetration of the neutral cluster at the higher collision energies and an evaporative evolution of the cluster ion at lower collision energies.

Acidification counteracts negative effects of warming on diatom silicification

KAUST Repository

Coello-Camba, Alexandra; Agusti, Susana

2016-01-01

Diatoms are a significant group contributing up to 40 % of annual primary production in the oceans. They have a special siliceous cell wall that, acting as a ballast, plays a key role in the sequestration of global carbon and silica. Diatoms dominate primary production in the Arctic Ocean, where global climate change is causing increases in water temperature and in the partial pressure of CO2 (pCO2). Here we show that as water temperature increases diatoms become stressed, grow to smaller sizes, and decrease their silicification rates. But at higher pCO2, as the pH of seawater decreases, silica incorporation rates are increased. In a future warmer Arctic ocean diatoms may have a competitive advantage under increased ocean acidification, as increased pCO2 counteracts the adverse effects of increasing temperature on silicification and buffers its consequences in the biogeochemical cycles of carbon and silica.

Acidification counteracts negative effects of warming on diatom silicification

KAUST Repository

Coello-Camba, Alexandra

2016-10-24

Diatoms are a significant group contributing up to 40 % of annual primary production in the oceans. They have a special siliceous cell wall that, acting as a ballast, plays a key role in the sequestration of global carbon and silica. Diatoms dominate primary production in the Arctic Ocean, where global climate change is causing increases in water temperature and in the partial pressure of CO2 (pCO2). Here we show that as water temperature increases diatoms become stressed, grow to smaller sizes, and decrease their silicification rates. But at higher pCO2, as the pH of seawater decreases, silica incorporation rates are increased. In a future warmer Arctic ocean diatoms may have a competitive advantage under increased ocean acidification, as increased pCO2 counteracts the adverse effects of increasing temperature on silicification and buffers its consequences in the biogeochemical cycles of carbon and silica.

Automated Diatom Analysis Applied to Traditional Light Microscopy: A Proof-of-Concept Study

Science.gov (United States)

Little, Z. H. L.; Bishop, I.; Spaulding, S. A.; Nelson, H.; Mahoney, C.

2017-12-01

Diatom identification and enumeration by high resolution light microscopy is required for many areas of research and water quality assessment. Such analyses, however, are both expertise and labor-intensive. These challenges motivate the need for an automated process to efficiently and accurately identify and enumerate diatoms. Improvements in particle analysis software have increased the likelihood that diatom enumeration can be automated. VisualSpreadsheet software provides a possible solution for automated particle analysis of high-resolution light microscope diatom images. We applied the software, independent of its complementary FlowCam hardware, to automated analysis of light microscope images containing diatoms. Through numerous trials, we arrived at threshold settings to correctly segment 67% of the total possible diatom valves and fragments from broad fields of view. (183 light microscope images were examined containing 255 diatom particles. Of the 255 diatom particles present, 216 diatoms valves and fragments of valves were processed, with 170 properly analyzed and focused upon by the software). Manual analysis of the images yielded 255 particles in 400 seconds, whereas the software yielded a total of 216 particles in 68 seconds, thus highlighting that the software has an approximate five-fold efficiency advantage in particle analysis time. As in past efforts, incomplete or incorrect recognition was found for images with multiple valves in contact or valves with little contrast. The software has potential to be an effective tool in assisting taxonomists with diatom enumeration by completing a large portion of analyses. Benefits and limitations of the approach are presented to allow for development of future work in image analysis and automated enumeration of traditional light microscope images containing diatoms.

Measurement of the density profile of pure and seeded molecular beams by femtosecond ion imaging

NARCIS (Netherlands)

Meng, C.; Janssen, M.H.M.

2015-01-01

Here, we report on femtosecond ion imaging experiments to measure the density profile of a pulsed supersonic molecular beam. Ion images are measured for both a molecular beam and bulk gas under identical experimental conditions via femtosecond multiphoton ionization of Xe atoms. We report the

Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.

Directory of Open Access Journals (Sweden)

Jonas Zimmermann

Full Text Available DNA barcoding uses a short fragment of a DNA sequence to identify a taxon. After obtaining the target sequence it is compared to reference sequences stored in a database to assign an organism name to it. The quality of data in the reference database is the key to the success of the analysis. In the here presented study, multiple types of data have been combined and critically examined in order to create best practice guidelines for taxonomic reference libraries for environmental barcoding. 70 unialgal diatom strains from Berlin waters have been established and cultured to obtain morphological and molecular data. The strains were sequenced for 18S V4 rDNA (the pre-Barcode for protists as well as rbcL data, and identified by microscopy. LM and for some strains also SEM pictures were taken and physical vouchers deposited at the BGBM. 37 freshwater taxa from 15 naviculoid diatom genera were identified. Four taxa from the genera Amphora, Mayamaea, Planothidium and Stauroneis are described here as new. Names, molecular, morphological and habitat data as well as additional images of living cells are also available electronically in the AlgaTerra Information System. All reference sequences (or reference barcodes presented here are linked to voucher specimens in order to provide a complete chain of evidence back to the formal taxonomic literature.

A synthesis of post-glacial diatom records from Lake Baikal

Science.gov (United States)

Bradbury, J. Platt; Bezrukova, E.; Chernyaeva, G.; Colman, S.M.; Khursevich, G.; King, J.W.; Likoshway, Ye. V.

1994-01-01

The biostratigraphy of fossil diatoms contributes important chronologic, paleolimnologic, and paleoclimatic information from Lake Baikal in southeastern Siberia. Diatoms are the dominant and best preserved microfossils in the sediments, and distinctive assemblages and species provide inter-core correlations throughout the basin at millennial to centennial scales, in both high and low sedimentation-rate environments. Distributions of unique species, once dated by radiocarbon, allow diatoms to be used as dating tools for the Holocene history of the lake.Diatom, pollen, and organic geochemical records from site 305, at the foot of the Selenga Delta, provide a history of paleolimnologic and paleoclimatic changes from the late glacial (15 ka) through the Holocene. Before 14 ka diatoms were very rare, probably because excessive turbidity from glacial meltwater entering the lake impeded productivity. Between 14 and 12 ka, lake productivity increased, perhaps as strong winds promoted deep mixing and nutrient regeneration. Pollen evidence suggests a cold shrub — steppe landscape dominated the central Baikal depression at this time. As summer insolation increased, conifers replaced steppe taxa, but diatom productivity declined between 11 and 9 ka perhaps as a result of increased summer turbidity resulting from violent storm runoff entering the lake via short, steep drainages. After 8 ka, drier, but more continental climates prevailed, and the modern diatom flora of Lake Baikal came to prominence.On Academician Ridge, a site of slow sedimentation rates, Holocene diatom assemblages at the top of 10-m cores reappear at deeper levels suggesting that such cores record at least two previous interglacial (or interstadial?) periods. Nevertheless, distinctive species that developed prior to the last glacial period indicate that the dynamics of nutrient cycling in Baikal and the responsible regional climatic environments were not entirely analogous to Holocene conditions. During

Molecular adaptations to phosphorus deprivation and comparison with nitrogen deprivation responses in the diatom Phaeodactylum tricornutum.

Science.gov (United States)

Alipanah, Leila; Winge, Per; Rohloff, Jens; Najafi, Javad; Brembu, Tore; Bones, Atle M

2018-01-01

Phosphorus, an essential element for all living organisms, is a limiting nutrient in many regions of the ocean due to its fast recycling. Changes in phosphate (Pi) availability in aquatic systems affect diatom growth and productivity. We investigated the early adaptive mechanisms in the marine diatom Phaeodactylum tricornutum to P deprivation using a combination of transcriptomics, metabolomics, physiological and biochemical experiments. Our analysis revealed strong induction of gene expression for proteins involved in phosphate acquisition and scavenging, and down-regulation of processes such as photosynthesis, nitrogen assimilation and nucleic acid and ribosome biosynthesis. P deprivation resulted in alterations of carbon allocation through the induction of the pentose phosphate pathway and cytosolic gluconeogenesis, along with repression of the Calvin cycle. Reorganization of cellular lipids was indicated by coordinated induced expression of phospholipases, sulfolipid biosynthesis enzymes and a putative betaine lipid biosynthesis enzyme. A comparative analysis of nitrogen- and phosphorus-deprived P. tricornutum revealed both common and distinct regulation patterns in response to phosphate and nitrate stress. Regulation of central carbon metabolism and amino acid metabolism was similar, whereas unique responses were found in nitrogen assimilation and phosphorus scavenging in nitrogen-deprived and phosphorus-deprived cells, respectively.

Iron Availability Influences Silicon Isotope Fractionation in Two Southern Ocean Diatoms (Proboscia inermis and Eucampia antarctica and a Coastal Diatom (Thalassiosira pseudonana

Directory of Open Access Journals (Sweden)

Scott Meyerink

2017-07-01

Full Text Available The fractionation of silicon (Si isotopes was measured in two Southern Ocean diatoms (Proboscia inermis and Eucampia Antarctica and a coastal diatom (Thalassiosira pseudonana that were grown under varying iron (Fe concentrations. Varying Fe concentrations had no effect on the Si isotope enrichment factor (ε in T. pseudonana, whilst E. Antarctica and P. inermis exhibited significant variations in the value of ε between Fe-replete and Fe-limited conditions. Mean ε values in P. inermis and E. Antarctica decreased from (± 1SD −1.11 ± 0.15‰ and −1.42 ± 0.41 ‰ (respectively under Fe-replete conditions, to −1.38 ± 0.27 ‰ and −1.57 ± 0.5 ‰ (respectively under Fe-limiting conditions. These variations likely arise from adaptations in diatoms arising from the nutrient status of their environment. T. pseudonana is a coastal clone typically accustomed to low Si but high Fe conditions whereas E. Antarctica and P. inermis are typically accustomed to High Si, High nitrate low Fe conditions. Growth induced variations in silicic acid (Si(OH4 uptake arising from Fe-limitation is the likely mechanism leading to Si-isotope variability in E. Antarctica and P. inermis. The multiplicative effects of species diversity and resource limitation (e.g., Fe on Si-isotope fractionation in diatoms can potentially alter the Si-isotope composition of diatom opal in diatamaceous sediments and sea surface Si(OH4. This work highlights the need for further in vitro studies into intracellular mechanisms involved in Si(OH4 uptake, and the associated pathways for Si-isotope fractionation in diatoms.

Fluxes of diatoms in the Dona Paula Bay, west coast of India

Digital Repository Service at National Institute of Oceanography (India)

Garg, A.; Bhaskar, P.V.

of POC and diatom carbon was 251 and 0.39 mg C m sup(-2) day sup(-1), respectively. The diatom carbon accounted for 0.15% of the POC flux. Mass flux of diatoms showed significant negative correlation with the concentration of nitrate and phosphate...

Seasonal effects of cadmium accumulation in periphytic diatom communities of freshwater biofilms

International Nuclear Information System (INIS)

Thi Thuy Duong; Morin, Soizic; Herlory, Olivier; Feurtet-Mazel, Agnes; Coste, Michel; Boudou, Alain

2008-01-01

The relationships between diatom species and cadmium (Cd) accumulated in biofilms of the Riou-Mort River (SW, France) were studied in July 2004 and March 2005. Biofilms were sampled from artificial substrates immersed along a metallic pollution gradient during 20 days. Dynamics of diatom communities and cadmium accumulation were followed by collecting samples after 4, 7, 14 and 20 days of biofilm colonization. Cd accumulation in biofilms during experiment was significantly higher in Cd polluted station (Joanis) than in reference station (Firmi) for both seasons. Periphytic diatom composition varied between sites and seasons. At Firmi station, seasonal dynamics of diatom communities were stable with the dominance of Cyclotella meneghiniana and Melosira varians in July and Surirellabrebissonnii and Navicula gregaria in March. At Joanis station, diatom communities mainly responded to high levels of metal by a high proportion of small, adnate species. Positive correlations between Eolimna minima, Nitzschia palea, Encyonema minutum, Surirella angusta, and Gomphonema parvulum and cadmium accumulation were observed, indicating that these species are tolerant to high levels of cadmium. On the other hand, negative correlations of C. meneghiniana, N. gregaria, Navicula lanceolata, M. varians and Nitzschia dissipata with cadmium qualify them as sensitive diatom species. Periphytic diatom composition through the presence of specific species highlight metal tolerant indicator diatom groups which will be meaningful for biomonitoring pollution in natural aquatic systems

Seasonal effects of cadmium accumulation in periphytic diatom communities of freshwater biofilms

Energy Technology Data Exchange (ETDEWEB)

Thi Thuy Duong [Institute of Environmental Technology, Vietnamese Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay, Hanoi (Viet Nam); Universite de Bordeaux 1, CNRS, UMR 5805 EPOC, Place du Dr Peyneau, 33120 Arcachon (France)], E-mail: duongthuy0712@yahoo.com; Morin, Soizic [Cemagref, UR REBX, 50 avenue de Verdun, F-33612 Cestas cedex (France); Herlory, Olivier [Universite de Bordeaux 1, CNRS, UMR 5805 EPOC, Place du Dr Peyneau, 33120 Arcachon (France); Feurtet-Mazel, Agnes [Universite de Bordeaux 1, CNRS, UMR 5805 EPOC, Place du Dr Peyneau, 33120 Arcachon (France)], E-mail: a.feurtet-mazel@epoc.u-bordeaux1.fr; Coste, Michel [Cemagref, UR REBX, 50 avenue de Verdun, F-33612 Cestas cedex (France); Boudou, Alain [Universite de Bordeaux 1, CNRS, UMR 5805 EPOC, Place du Dr Peyneau, 33120 Arcachon (France)

2008-10-20

The relationships between diatom species and cadmium (Cd) accumulated in biofilms of the Riou-Mort River (SW, France) were studied in July 2004 and March 2005. Biofilms were sampled from artificial substrates immersed along a metallic pollution gradient during 20 days. Dynamics of diatom communities and cadmium accumulation were followed by collecting samples after 4, 7, 14 and 20 days of biofilm colonization. Cd accumulation in biofilms during experiment was significantly higher in Cd polluted station (Joanis) than in reference station (Firmi) for both seasons. Periphytic diatom composition varied between sites and seasons. At Firmi station, seasonal dynamics of diatom communities were stable with the dominance of Cyclotella meneghiniana and Melosira varians in July and Surirellabrebissonnii and Navicula gregaria in March. At Joanis station, diatom communities mainly responded to high levels of metal by a high proportion of small, adnate species. Positive correlations between Eolimna minima, Nitzschia palea, Encyonema minutum, Surirella angusta, and Gomphonema parvulum and cadmium accumulation were observed, indicating that these species are tolerant to high levels of cadmium. On the other hand, negative correlations of C. meneghiniana, N. gregaria, Navicula lanceolata, M. varians and Nitzschia dissipata with cadmium qualify them as sensitive diatom species. Periphytic diatom composition through the presence of specific species highlight metal tolerant indicator diatom groups which will be meaningful for biomonitoring pollution in natural aquatic systems.

Colonization of diatom aggregates by the dinoflagellate Noctiluca scintillans

DEFF Research Database (Denmark)

Tiselius, P.; Kiørboe, Thomas

1998-01-01

coagulation of diatom cells and not by mucus feeding behavior of N. scintillans. N. scintillans can be positively buoyant, and estimates of encounter rates between N. scintillans and diatom aggregates during ascent demonstrates that this mechanism is sufficient to account for the observed colonization...

Components of the Bond Energy in Polar Diatomic Molecules, Radicals, and Ions Formed by Group-1 and Group-2 Metal Atoms.

Science.gov (United States)

Yu, Haoyu; Truhlar, Donald G

2015-07-14

Although many transition metal complexes are known to have high multireference character, the multireference character of main-group closed-shell singlet diatomic molecules like BeF, CaO, and MgO has been less studied. However, many group-1 and group-2 diatomic molecules do have multireference character, and they provide informative systems for studying multireference character because they are simpler than transition metal compounds. The goal of the present work is to understand these multireference systems better so that, ultimately, we can apply what we learn to more complicated multireference systems and to the design of new exchange-correlation functionals for treating multireference systems more adequately. Fourteen main-group diatomic molecules and one triatomic molecule (including radicals, cations, and anions, as well as neutral closed-shell species) have been studied for this article. Eight of these molecules contain a group-1 element, and six contain a group-2 element. Seven of these molecules are multireference systems, and eight of them are single-reference systems. Fifty-three exchange-correlation functionals of 11 types [local spin-density approximation (LSDA), generalized gradient approximation (GGA), nonseparable gradient approximation (NGA), global-hybrid GGA, meta-GGA, meta-NGA, global-hybrid meta GGA, range-separated hybrid GGA, range-separated hybrid meta-GGA, range-separated hybrid meta-NGA, and DFT augmented with molecular mechanics damped dispersion (DFT-D)] and the Hartree-Fock method have been applied to calculate the bond distance, bond dissociation energy (BDE), and dipole moment of these molecules. All of the calculations are converged to a stable solution by allowing the symmetry of the Slater determinant to be broken. A reliable functional should not only predict an accurate BDE but also predict accurate components of the BDE, so each bond dissociation energy has been decomposed into ionization potential (IP) of the electropositive

Diatom feeding across trophic guilds in tidal flat nematodes, and the importance of diatom cell size

Science.gov (United States)

Moens, Tom; Vafeiadou, Anna-Maria; De Geyter, Ellen; Vanormelingen, Pieter; Sabbe, Koen; De Troch, Marleen

2014-09-01

We examine the capacity of nematodes from three feeding types (deposit feeder, epistrate feeder, predator) to utilize microphytobenthos (MPB), and assess whether diatom cell size and consumer body size are important drivers of their feeding. We analyzed natural stable isotope ratios of carbon and nitrogen in abundant nematode genera and a variety of carbon sources at an estuarine intertidal flat. All nematodes had δ13C indicating that MPB is their major carbon source. δ15N, however, demonstrated that only one deposit and one epistrate feeder genus obtained most of their carbon from direct grazing on MPB, whereas other deposit feeders and predators obtained at least part of their carbon by predation on MPB grazers. We then performed a microcosm experiment in which equal cell numbers of each of three differently sized strains of the pennate diatom Seminavis were offered as food to four, one and one genera of deposit feeders, epistrate feeders and predators, respectively. Previous studies have shown that all but the epistrate feeder ingest whole diatoms, whereas the epistrate feeder pierces cells and sucks out their contents. Most genera showed markedly higher carbon absorption from medium and large cells than from small ones. When considering the number of cells consumed, however, none of the nematodes which ingest whole cells exhibited a clear preference for any specific diatom size. The epistrate feeder was the smallest nematode taxon considered here, yet it showed a marked preference for large cells. These results highlight that the feeding mechanism is much more important than consumer size as a driver of particle size selection in nematodes grazing MPB.

Experimental investigation of the formation of negative hydrogen ions in collisions between positive ions and atomic or molecular targets

International Nuclear Information System (INIS)

Lattouf, Elie

2013-01-01

The formation of the negative hydrogen ion (H - ) in collisions between a positive ion and a neutral atomic or molecular target is studied experimentally at impact energies of a few keV. The doubly-differential cross sections for H - formation are measured as a function of the kinetic energy and emission angle for the collision systems OH + + Ar and O + + H 2 O at 412 eV/a.m.u. These H - ions can be emitted at high energies (keV) in hard quasi-elastic two-body collisions involving a large momentum transfer to the H center. However, H - anions are preferentially emitted at low energy (eV) due to soft many-body (≥ 2) collisions resulting in a low momentum transfer. The formation of H - ions by electron capture follows excitation or ionization of the molecule. The molecular fragmentation dynamics is modeled to simulate the emission of H - ions. The overall good agreement between the simulation and the experiment leads to the understanding of most of the experimental observations. (author) [fr

Diatom paleoecology Pass Key core 37, Everglades National Park, Florida Bay

Science.gov (United States)

Pyle, Laura; Cooper, S.R.; Huvane, J.K.

1998-01-01

During the 20th century, there have been large-scale anthropogenic modifications to the South Florida ecosystem. The effects of these changes on Florida Bay and its biological communities are currently of political and scientific interest. This study is part of a larger effort to reconstruct the history of environmental changes in the bay, using paleoecological techniques. We are using diatom indicators preserved in Florida Bay sediments to infer long-term water quality, productivity, nutrient, and salinity changes. We are also obtaining information concerning the natural variability of the ecosystem. Diatoms are microscopic algae, the remains of which are generally well preserved in sediments, and their distributions are closely linked to water quality. Diatoms were extracted from a 70-cm sediment core collected from the Pass Key mudbank of Florida Bay by the U.S. Geological Survey. Between 300-500 diatom valves from each of 15 core samples were identified and counted. Estimates of absolute abundance, species richness, Shannon-Wiener diversity, and centric:pennate ratios were calculated for each sample that was counted. Information on the ecology of the diatom species is presented, and changes in diatom community composition are evaluated. Samples contained an average of four million diatom valves per gram of sediment. Major changes in the diatom community are evident down core. These include increases in the percent abundance of marine diatoms in the time period represented by the core, probably the result of increasing salinity at Pass Key. Benthic diatoms become less abundant in the top half of the core. This may be related to a number of factors including the die-off of sea grass beds or increased turbidity of the water column. Once the chronology of the Pass Key core 37 is established, these down-core changes can be related to historical events and compared with other indicators in the sedimentary record that are currently being investigated by U.S Geological

Development of a Submillimeter Multipass Spectrometer for the Study of Molecular Ions

Science.gov (United States)

Carroll, A.; Rocher, B.; Laas, J. C.; Deprince, B. A.; Hays, B.; Weaver, S. L. Widicus; Lang, S.

2012-06-01

We have developed a multipass spectrometer for the submillimeter spectral region that is being used to study molecular ions through gas phase spectroscopy. The optical configuration is based on the design of Perry and coworkers that was implemented in the optical regime. To our knowledge, this is the first implementation of this optical configuration at long wavelengths. The setup involves two nearly concentric spherical mirrors that focus the multiple beam passes into a small area, or ``waist'', in the middle of the sample chamber. A supersonic molecular beam is coupled to the setup so that the molecular beam crosses the optical path at the waist. Initial studies have focused on neutral test molecules to probe the physical properties of the molecular beam under various arrangements of the molecular source relative to the optical path. Current studies focus on coupling a plasma discharge source to the setup to enable the study of molecular ions. Here we present the design of this instrument, compare the spectrometer capabilities to a traditional single pass spectrometer, and discuss the results of initial spectroscopic studies.

Diatom species abundance and morphologically-based dissolution proxies in coastal Southern Ocean assemblages

Science.gov (United States)

Warnock, Jonathan P.; Scherer, Reed P.

2015-07-01

Taphonomic processes alter diatom assemblages in sediments, thus potentially negatively impacting paleoclimate records at various rates across space, time, and taxa. However, quantitative taphonomic data is rarely included in diatom-based paleoenvironmental reconstructions and no objective standard exists for comparing diatom dissolution in sediments recovered from marine depositional settings, including the Southern Ocean's opal belt. Furthermore, identifying changes to diatom dissolution through time can provide insight into the efficiency of both upper water column nutrient recycling and the biological pump. This is significant in that reactive metal proxies (e.g. Al, Ti) in the sediments only account for post-depositional dissolution, not the water column where the majority of dissolution occurs. In order to assess the range of variability of responses to dissolution in a typical Southern Ocean diatom community and provide a quantitative guideline for assessing taphonomic variability in diatoms recovered from core material, a sediment trap sample was subjected to controlled, serial dissolution. By evaluating dissolution-induced changes to diatom species' relative abundance, three preservational categories of diatoms have been identified: gracile, intermediate, and robust. The relative abundances of these categories can be used to establish a preservation grade for diatom assemblages. However, changes to the relative abundances of diatom species in sediment samples may reflect taphonomic or ecological factors. In order to address this complication, relative abundance changes have been tied to dissolution-induced morphological change to the areolae of Fragilariopsis curta, a significant sea-ice indicator in Southern Ocean sediments. This correlation allows differentiation between gracile species loss to dissolution versus ecological factors or sediment winnowing. These results mirror a similar morphological dissolution index from a parallel study utilizing

Diatoms in Liyu Lake, Eastern Taiwan

Directory of Open Access Journals (Sweden)

Liang-Chi Wang

2010-09-01

Full Text Available This study described the diatoms appeared in the sediments of Liyu Lake, a lowland natural lake situated at Hualen, eastern Taiwan. A total of 50 species was found in the sediments of this eutrophic lake. In them, 8 species were reported for the first time in Taiwan. They are: Cymbella thienemannii, Navicula absoluta, Navicula bacillum, Frustulia rhomboides var. crassinervia, Gyrosigma procerum, Nitzschia paleacea Epithemia smithii and Eunotia subarcuatioides. The ultrastructures of each species were described on the basis of observations under a scanning electron microscope. The ecological implications of the occurrence of these diatom species in this lake were inferred.

Nonlinear effects in defect production by atomic and molecular ion implantation

International Nuclear Information System (INIS)

David, C.; Dholakia, Manan; Chandra, Sharat; Nair, K. G. M.; Panigrahi, B. K.; Amirthapandian, S.; Amarendra, G.; Varghese Anto, C.; Santhana Raman, P.; Kennedy, John

2015-01-01

This report deals with studies concerning vacancy related defects created in silicon due to implantation of 200 keV per atom aluminium and its molecular ions up to a plurality of 4. The depth profiles of vacancy defects in samples in their as implanted condition are carried out by Doppler broadening spectroscopy using low energy positron beams. In contrast to studies in the literature reporting a progressive increase in damage with plurality, implantation of aluminium atomic and molecular ions up to Al 3 , resulted in production of similar concentration of vacancy defects. However, a drastic increase in vacancy defects is observed due to Al 4 implantation. The observed behavioural trend with respect to plurality has even translated to the number of vacancies locked in vacancy clusters, as determined through gold labelling experiments. The impact of aluminium atomic and molecular ions simulated using MD showed a monotonic increase in production of vacancy defects for cluster sizes up to 4. The trend in damage production with plurality has been explained on the basis of a defect evolution scheme in which for medium defect concentrations, there is a saturation of the as-implanted damage and an increase for higher defect concentrations

Acceleration of cluster and molecular ions by TIARA 3 MV tandem accelerator

CERN Document Server

Saitoh, Y; Tajima, S

2000-01-01

We succeeded in accelerating molecular and cluster ions (B sub 2 sub - sub 4 , C sub 2 sub - sub 1 sub 0 , O sub 2 , Al sub 2 sub - sub 4 , Si sub 2 sub - sub 4 , Cu sub 2 sub - sub 3 , Au sub 2 sub - sub 3 , LiF, and AlO) to MeV energies with high-intensity beam currents by means of a 3 MV tandem accelerator in the TIARA facility. These cluster ions were generated by a cesium sputter-type negative ion source. We tested three types of carbon sputter cathodes in which graphite powder was compressed with different pressures. The pressure difference affected the generating ratio of clusters generated to single atom ions extracted from the source and it appeared that the high-density cathode was suitable. We also investigated the optimum gas pressure for charge exchange in the tandem high-voltage terminal. Clusters of larger size tend to require lower pressure than do smaller ones. In addition, we were able to obtain doubly charged AlO molecular ions. (authors)

Insight into the Supramolecular Architecture of Intact Diatom Biosilica from DNP-Supported Solid-State NMR Spectroscopy.

Science.gov (United States)

Jantschke, Anne; Koers, Eline; Mance, Deni; Weingarth, Markus; Brunner, Eike; Baldus, Marc

2015-12-07

Diatom biosilica is an inorganic/organic hybrid with interesting properties. The molecular architecture of the organic material at the atomic and nanometer scale has so far remained unknown, in particular for intact biosilica. A DNP-supported ssNMR approach assisted by microscopy, MS, and MD simulations was applied to study the structural organization of intact biosilica. For the first time, the secondary structure elements of tightly biosilica-associated native proteins in diatom biosilica were characterized in situ. Our data suggest that these proteins are rich in a limited set of amino acids and adopt a mixture of random-coil and β-strand conformations. Furthermore, biosilica-associated long-chain polyamines and carbohydrates were characterized, thereby leading to a model for the supramolecular organization of intact biosilica. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electric dipole moments and chemical bonding of diatomic alkali-alkaline earth molecules.

Science.gov (United States)

Pototschnig, Johann V; Hauser, Andreas W; Ernst, Wolfgang E

2016-02-17

We investigate the properties of alkali-alkaline earth diatomic molecules in the lowest Σ(+) states of the doublet and quartet multiplicity by ab initio calculations. In all sixteen cases studied, the permanent electric dipole moment points in opposite directions for the two spin states. This peculiarity can be explained by molecular orbital theory. We further discuss dissociation energies and bond distances. We analyze trends and provide an empirically motivated model for the prediction of the permanent electric dipole moment for combinations of alkali and alkaline earth atoms not studied in this work.

Chronic Iron Limitation Confers Transient Resistance to Oxidative Stress in Marine Diatoms1

Science.gov (United States)

Graff van Creveld, Shiri; Rosenwasser, Shilo; Vardi, Assaf

2016-01-01

Diatoms are single-celled, photosynthetic, bloom-forming algae that are responsible for at least 20% of global primary production. Nevertheless, more than 30% of the oceans are considered “ocean deserts” due to iron limitation. We used the diatom Phaeodactylum tricornutum as a model system to explore diatom’s response to iron limitation and its interplay with susceptibility to oxidative stress. By analyzing physiological parameters and proteome profiling, we defined two distinct phases: short-term (5 d, phase II) iron limitation. While at phase I no significant changes in physiological parameters were observed, molecular markers for iron starvation, such as Iron Starvation Induced Protein and flavodoxin, were highly up-regulated. At phase II, down-regulation of numerous iron-containing proteins was detected in parallel to reduction in growth rate, chlorophyll content, photosynthetic activity, respiration rate, and antioxidant capacity. Intriguingly, while application of oxidative stress to phase I and II iron-limited cells similarly oxidized the reduced glutathione (GSH) pool, phase II iron limitation exhibited transient resistance to oxidative stress, despite the down regulation of many antioxidant proteins. By comparing proteomic profiles of P. tricornutum under iron limitation and metatranscriptomic data of an iron enrichment experiment conducted in the Pacific Ocean, we propose that iron-limited cells in the natural environment resemble the phase II metabolic state. These results provide insights into the trade-off between optimal growth rate and susceptibility to oxidative stress in the response of diatoms to iron quota in the marine environment. PMID:27503604

The health of benthic diatom assemblages in lower stretch

Indian Academy of Sciences (India)

This study examines the ecological state of epilithic diatom assemblages along the lower stretch of Mandakini, a glacier-fed Himalayan river. The diatoms were sampled at four stations during winter and summer, only once in each season. Valve counts were obtained from Naphrax mounts prepared from each sample.

Experimental Investigation of Impact-Induced Molecular Desorption by 4.2 MeV/u Pb ions

CERN Document Server

Chanel, M; Laurent, Jean Michel; Madsen, N; Mahner, E

2001-01-01

In preparation for the heavy ion program of the LHC, accumulation and cooling test with lead ion beams have been performed in the LEAR storage ring. These tests have revealed that due to the unexpected, large outgassing of the vacuum system, the dynamic pressure of the ring could not be maintained low enough to reach the required beam intensities. To determine the actions necessary to lower the dynamic pressure rise, an experimental program has been initiated for measuring the molecular desorption yields of stainless steel vacuum chambers by the impact of 4.2 MeV/u lead ions with the charge states +27 and +53. The test chambers were exposed either at grazing or at perpendicular incidence. Different surface treatments are reported in terms of the molecular desorption yields for H2, CH4, CO and CO2. Unpexpected large values of molecular yields per incident ion up to 2x104 molecules/ion have been observed. The implications of these results for the vacuum system of the future ion accumulator ring (LEIR) and possi...

Biochemical Composition and Assembly of Biosilica-associated Insoluble Organic Matrices from the Diatom Thalassiosira pseudonana.

Science.gov (United States)

Kotzsch, Alexander; Pawolski, Damian; Milentyev, Alexander; Shevchenko, Anna; Scheffel, André; Poulsen, Nicole; Shevchenko, Andrej; Kröger, Nils

2016-03-04

The nano- and micropatterned biosilica cell walls of diatoms are remarkable examples of biological morphogenesis and possess highly interesting material properties. Only recently has it been demonstrated that biosilica-associated organic structures with specific nanopatterns (termed insoluble organic matrices) are general components of diatom biosilica. The model diatom Thalassiosira pseudonana contains three types of insoluble organic matrices: chitin meshworks, organic microrings, and organic microplates, the latter being described in the present study for the first time. To date, little is known about the molecular composition, intracellular assembly, and biological functions of organic matrices. Here we have performed structural and functional analyses of the organic microrings and organic microplates from T. pseudonana. Proteomics analysis yielded seven proteins of unknown function (termed SiMat proteins) together with five known silica biomineralization proteins (four cingulins and one silaffin). The location of SiMat1-GFP in the insoluble organic microrings and the similarity of tyrosine- and lysine-rich functional domains identifies this protein as a new member of the cingulin protein family. Mass spectrometric analysis indicates that most of the lysine residues of cingulins and the other insoluble organic matrix proteins are post-translationally modified by short polyamine groups, which are known to enhance the silica formation activity of proteins. Studies with recombinant cingulins (rCinY2 and rCinW2) demonstrate that acidic conditions (pH 5.5) trigger the assembly of mixed cingulin aggregates that have silica formation activity. Our results suggest an important role for cingulins in the biogenesis of organic microrings and support the hypothesis that this type of insoluble organic matrix functions in biosilica morphogenesis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Molecular projectile effects for kinetic electron emission from carbon- and metal-surfaces bombarded by slow hydrogen ions

Science.gov (United States)

Cernusca, S.; Winter, HP.; Aumayr, F.; Díez Muiño, R.; Juaristi, J. I.

2003-04-01

Total yields for kinetic electron emission (KE) have been determined for impact of hydrogen monomer-, dimer- and trimer-ions (impact energy armour in magnetic fusion devices. The data are compared with KE yields for impact of same projectile ions on atomically clean highly oriented pyrolytic graphite and polycrystalline gold. We discuss KE yields for the different targets if bombarded by equally fast molecular and atomic ions in view to "projectile molecular effects" (different yields per proton for equally fast atomic and molecular ions), which are expected from calculated electronic projectile energy losses in these target materials.

Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments.

Science.gov (United States)

Broman, Elias; Sachpazidou, Varvara; Dopson, Mark; Hylander, Samuel

2017-10-11

An important characteristic of marine sediments is the oxygen concentration that affects many central metabolic processes. There has been a widespread increase in hypoxia in coastal systems (referred to as 'dead zones') mainly caused by eutrophication. Hence, it is central to understand the metabolism and ecology of eukaryotic life in sediments during changing oxygen conditions. Therefore, we sampled coastal 'dead zone' Baltic Sea sediment during autumn and spring, and analysed the eukaryotic metatranscriptome from field samples and after incubation in the dark under oxic or anoxic conditions. Bacillariophyta (diatoms) dominated the eukaryotic metatranscriptome in spring and were also abundant during autumn. A large fraction of the diatom RNA reads was associated with the photosystems suggesting a constitutive expression in darkness. Microscope observation showed intact diatom cells and these would, if hatched, represent a significant part of the pelagic phytoplankton biomass. Oxygenation did not significantly change the relative proportion of diatoms nor resulted in any major shifts in metabolic 'signatures'. By contrast, diatoms rapidly responded when exposed to light suggesting that light is limiting diatom development in hypoxic sediments. Hence, it is suggested that diatoms in hypoxic sediments are on 'standby' to exploit the environment if they reach suitable habitats. © 2017 The Author(s).

Investigation of the hydrodynamic behavior of diatom aggregates using particle image velocimetry.

Science.gov (United States)

Xiao, Feng; Li, Xiaoyan; Lam, Kitming; Wang, Dongsheng

2012-01-01

The hydrodynamic behavior of diatom aggregates has a significant influence on the interactions and flocculation kinetics of algae. However, characterization of the hydrodynamics of diatoms and diatom aggregates in water is rather difficult. In this laboratory study, an advanced visualization technique in particle image velocimetry (PIV) was employed to investigate the hydrodynamic properties of settling diatom aggregates. The experiments were conducted in a settling column filled with a suspension of fluorescent polymeric beads as seed tracers. A laser light sheet was generated by the PIV setup to illuminate a thin vertical planar region in the settling column, while the motions of particles were recorded by a high speed charge-coupled device (CCD) camera. This technique was able to capture the trajectories of the tracers when a diatom aggregate settled through the tracer suspension. The PIV results indicated directly the curvilinear feature of the streamlines around diatom aggregates. The rectilinear collision model largely overestimated the collision areas of the settling particles. Algae aggregates appeared to be highly porous and fractal, which allowed streamlines to penetrate into the aggregate interior. The diatom aggregates have a fluid collection efficiency of 10%-40%. The permeable feature of aggregates can significantly enhance the collisions and flocculation between the aggregates and other small particles including algal cells in water.

A simple digestion method with a Lefort aqua regia solution for diatom extraction.

Science.gov (United States)

Wang, Huipin; Liu, Yan; Zhao, Jian; Hu, Sunlin; Wang, Yuzhong; Liu, Chao; Zhang, Yanji

2015-01-01

Presence of diatoms in tissues has been considered as a significant sign of drowning. However, there are limitations in the present extraction methods. We developed a new digestion method using the Lefort aqua regia solution (3:1 nitric acid to hydrochloric acid) for diatom extraction and evaluated the digestive capability, diatom destruction, and diatoms' recovery of this new method. The kidney tissues from rabbit mixed with water rich in diatoms were treated by the Lefort aqua regia digestion method (n = 10) and the conventional acid digestion method (n = 10). The results showed that the digestive capability of Lefort aqua regia digestion method was superior to conventional acid digestion method (p 0.05). The Lefort aqua regia reagent is an improvement over the conventional acid digestion for recovery of diatoms from tissue samples. © 2014 American Academy of Forensic Sciences.

Rotational laser cooling of vibrationally and translationally cold molecular ions

DEFF Research Database (Denmark)

Staanum, Peter; Højbjerre, Klaus; Skyt, Peter Sandegaard

2010-01-01

Stationary molecules in well-defined internal states are of broad interest for physics and chemistry. In physics, this includes metrology 1, 2, 3 , quantum computing 4, 5 and many-body quantum mechanics 6, 7 , whereas in chemistry, state-prepared molecular targets are of interest for uni......-molecular reactions with coherent light fields 8, 9 , for quantum-state-selected bi-molecular reactions 10, 11, 12 and for astrochemistry 12 . Here, we demonstrate rotational ground-state cooling of vibrationally and translationally cold MgH+ ions, using a laser-cooling scheme based on excitation of a single...

Laser induced fluorescence of trapped molecular ions

International Nuclear Information System (INIS)

Winn, J.S.

1980-10-01

Laser induced fluoresence (LIF) spectra (laser excitation spectra) are conceptually among the most simple spectra to obtain. One need only confine a gaseous sample in a suitable container, direct a laser along one axis of the container, and monitor the sample's fluorescence at a right angle to the laser beam. As the laser wavelength is changed, the changes in fluorescence intensity map the absorption spectrum of the sample. (More precisely, only absorption to states which have a significant radiative decay component are monitored.) For ion spectroscopy, one could benefit in many ways by such an experiment. Most optical ion spectra have been observed by emission techniques, and, aside from the problems of spectral analysis, discharge emission methods often produce the spectra of many species, some of which may be unknown or uncertain. Implicit in the description of LIF given above is certainty as to the chemical identity of the carrier of the spectrum. This article describes a method by which the simplifying aspects of LIF can be extended to molecular ions

Ion Flux Measurements in Electron Beam Produced Plasmas in Atomic and Molecular Gases

Science.gov (United States)

Walton, S. G.; Leonhardt, D.; Blackwell, D. D.; Murphy, D. P.; Fernsler, R. F.; Meger, R. A.

2001-10-01

In this presentation, mass- and time-resolved measurements of ion fluxes sampled from pulsed, electron beam-generated plasmas will be discussed. Previous works have shown that energetic electron beams are efficient at producing high-density plasmas (10^10-10^12 cm-3) with low electron temperatures (Te < 1.0 eV) over the volume of the beam. Outside the beam, the plasma density and electron temperature vary due, in part, to ion-neutral and electron-ion interactions. In molecular gases, electron-ion recombination plays a significant role while in atomic gases, ion-neutral interactions are important. These interactions also determine the temporal variations in the electron temperature and plasma density when the electron beam is pulsed. Temporally resolved ion flux and energy distributions at a grounded electrode surface located adjacent to pulsed plasmas in pure Ar, N_2, O_2, and their mixtures are discussed. Measurements are presented as a function of operating pressure, mixture ratio, and electron beam-electrode separation. The differences in the results for atomic and molecular gases will also be discussed and related to their respective gas-phase kinetics.

Doping of magnetite nanoparticles facilitates clean harvesting of diatom oil as biofuel for sustainable energy

Science.gov (United States)

Kumar, Vikas; Singh, Ramesh; Thakur, Shipra; Ballabh Joshi, Khashti; Vinayak, Vandana

2018-04-01

Photosynthetic unicellular brown algae diatoms are considered as photobioreactors (PBRs) that synthesize and store oil in the form of lipid droplets and the much of the crude oil we use comes from fossil diatoms. The clean extraction of this crude oil from diatoms is difficult task. The construction of green chemical protocols for the clean separation of diatom oil from cells without killing or to harm the diatom cells is still in its primitive stage. In this report we would like to propose that facile doping of magnetite on diatoms can be used for clean oil separation in PBRs. We doped magnetite nanoparticles onto the surface of diatom Diadesmis confervaceae a diatom which oozes oil naturally. Doping magnetite onto diatoms can also facilitate easy separation of oil when cells are kept in an electromagnetic field. The cell wall of diatom besides having SiOH group has 281 amino acids of which 187–188 amino acids are conserved and are known for metal binding sites. The magnetite nanoparticles bind to the SiOH groups and metal binding sites of amino acids. The presence of appropriate amine functionalized linkers forming peptide aminosilane shells can further facilitate the binding of peptide/polypeptides which can be used in drug delivery. Besides this the magnetite doped diatoms have wide applications in removal of phosphates and chromium from waste water too.

Thermal characterization of Ag and Ag + N ion implanted ultra-high molecular weight polyethylene (UHMWPE)

Science.gov (United States)

Sokullu Urkac, E.; Oztarhan, A.; Tihminlioglu, F.; Kaya, N.; Ila, D.; Muntele, C.; Budak, S.; Oks, E.; Nikolaev, A.; Ezdesir, A.; Tek, Z.

2007-08-01

Most of total hip joints are composed of ultra-high molecular weight polyethylene (UHMWPE). However, as ultra-high molecular weight polyethylene is too stable in a body, wear debris may accumulate and cause biological response such as bone absorption and loosening of prosthesis. In this study, ultra-high molecular weight polyethylene samples were Ag and Ag + N hybrid ion implanted by using MEVVA ion implantation technique to improve its surface properties. Samples were implanted with a fluence of 1017 ion/cm2 and extraction voltage of 30 kV. Implanted and unimplanted samples were investigated by thermo-gravimetry analysis (TGA), differential scanning calorimetry (DSC), X-ray diffraction (XRD) analysis, scanning electron microscopy (SEM), optical microscopy (OM) and contact Angle measurement. Thermal characterization results showed that the ion bombardment induced an increase in the % crystallinity, onset and termination degradation temperatures of UHMWPE.

Hydrogen molecular ions for improved determination of fundamental constants

NARCIS (Netherlands)

Karr, J.-P.; Hilico, L.; Koelemeij, J.C.J.; Korobov, V.I.

2016-01-01

The possible use of high-resolution rovibrational spectroscopy of the hydrogen molecular ions H-2(+) and HD+ for an independent determination of several fundamental constants is analyzed. While these molecules had been proposed for the metrology of nuclear-to-electron mass ratios, we show that they

The transmission of fast molecular ions through thin foils

International Nuclear Information System (INIS)

Pietsch, W.J.; Gemmell, D.S.; Cooney, P.J.; Kanter, E.P.; Kurath, D.; Ratkowski, A.J.; Vager, Z.; Zabransky, B.J.

1980-01-01

We present new results on the transmission of fast molecular ions through thin foils and propose a mechanism for the transmission process. The main feature of the postulated mechanism is that a finite fraction of the incident molecular beam does not undergo a strong Coulomb explosion while traversing the foil. Because the emerging fragments are at large internuclear separations, there is an enhanced probability for the formation of bound, long-range, excited electronic states following electron capture at the rear surface of the target. (orig.)

Generalized extended Navier-Stokes theory: Multiscale spin relaxation in molecular fluids

DEFF Research Database (Denmark)

Hansen, Jesper Schmidt

2013-01-01

This paper studies the relaxation of the molecular spin angular velocity in the framework of generalized extended Navier-Stokes theory. Using molecular dynamics simulations, it is shown that for uncharged diatomic molecules the relaxation time decreases with increasing molecular moment of inertia...

Diatoms in acid mine drainage and their role in the formation of iron-rich stromatolites

Energy Technology Data Exchange (ETDEWEB)

Brake, S.S.; Hasiotis, S.T.; Dannelly, H.K. [Indiana State University, Terre Haute, IN (United States)

2004-08-01

Adverse conditions in the acid mine drainage (AMD) system at the Green Valley mine, Indiana, limit diatom diversity to one species, Nitzschia tubicola. It is present in three distinct microbial consortia: Euglena mutabilis-dominated biofilm, diatom-dominated biofilm, and diatom-exclusive biofilm. E. mutabilis dominates the most extensive biofilm, with lesser numbers of N. tubicola, other eukaryotes, and bacteria. Diatom-dominated biofilm occurs as isolated patches containing N. tubicola with minor fungal hyphae, filamentous algae, E. mutabilis, and bacteria. Diatom-exclusive biofilm is rare, composed entirely of N. tubicola. Diatom distribution is influenced by seasonal and intraseasonal changes in water temperature and chemistry. Diatoms are absent in winter due to cool water temperatures. In summer, isolated patchy communities are present due to warmer water temperatures. In 2001, the diatom community expanded its distribution following a major rainfall that temporarily diluted the effluent, creating hospitable conditions for diatom growth. After several weeks when effluent returned to preexisting conditions, the diatom biofilm retreated to isolated patches, and E. mutabilis biofilm flourished. Iron-rich stromatolites underlie the biofilms and consist of distinct laminae, recording spatial and temporal oscillations in physicochemical conditions and microbial activity. The stromatolites are composed of thin, wavy laminae with partially decayed E. mutabilis biofilm, representing microbial activity and iron precipitation under normal AMD conditions. Alternating with the wavy layers are thicker, porous, spongelike laminae composed of iron precipitated on and incorporated into radiating colonies of diatoms. These layers indicate episodic changes in water chemistry, allowing diatoms to temporarily dominate the system.

Theoretical Concepts in Molecular Photodissociation Dynamics

DEFF Research Database (Denmark)

Henriksen, Niels Engholm

1995-01-01

This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...

Diatomic infrared gas-dynamic laser

International Nuclear Information System (INIS)

Mckenzie, R.L.

1971-01-01

A laser is provided which utilizes the infrared vibration rotation transitions of a diatomic gas such as carbon monoxide. The laser action is produced by an active diatomic gas such as carbon monoxide mixed with a vibrationally resonant pumping gas such as nitrogen. In addition, a noble gas such as argon may be employed as a third gas in the mixture. The gas mixture contains from 1 to 80 vol percent of the active gas based on the pumping gas, and the third gas, if used, can constitute up to 90 percent of the total gas volume. A number of significantly different wavelengths can be produced by the laser. A single laser may contain several optical resonators at different locations, so that the desired wave length can be selected at will

Fossil diatoms imply common cometary origin of space-dust and the Polonnaruwa meteorite

Science.gov (United States)

Miyake, N.; Wallis, M. K.; Wickramasinghe, N. C.

2013-09-01

IDPs collected in 2001 at 40km altitude by cryosamplers studied via scanning electron microscopy and EDX were found to contain siliceous fibres and whiskers, some isolated but often embedded in a mineral matrix. The newly-arrived Polonnaruwa meteorite gives strong evidence for the hypothesis that they are fragments of diatoms agglomerating on solar system icy bodies. Diatom frustules and even whole diatom skeletons are identifiable within the meteorite. Specimens of a siliceous exoskeleton with multiple spines/whiskers have also been found, thought to be freshwater diatoms. As diatoms are dependent on a source of nitrogenous organics, the siliceous whiskers within IDPs would be an indicator of a photosynthesizing ecosystem, probably on a comet.

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

KAUST Repository

Mock, Thomas

2017-01-17

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

KAUST Repository

Mock, Thomas; Otillar, Robert P.; Strauss, Jan; McMullan, Mark; Paajanen, Pirita; Schmutz, Jeremy; Salamov, Asaf; Sanges, Remo; Toseland, Andrew; Ward, Ben J.; Allen, Andrew E.; Dupont, Christopher L.; Frickenhaus, Stephan; Maumus, Florian; Veluchamy, Alaguraj; Wu, Taoyang; Barry, Kerrie W.; Falciatore, Angela; Ferrante, Maria I.; Fortunato, Antonio E.; Glö ckner, Gernot; Gruber, Ansgar; Hipkin, Rachel; Janech, Michael G.; Kroth, Peter G.; Leese, Florian; Lindquist, Erika A.; Lyon, Barbara R.; Martin, Joel; Mayer, Christoph; Parker, Micaela; Quesneville, Hadi; Raymond, James A.; Uhlig, Christiane; Valas, Ruben E.; Valentin, Klaus U.; Worden, Alexandra Z.; Armbrust, E. Virginia; Clark, Matthew D.; Bowler, Chris; Green, Beverley R.; Moulton, Vincent; Oosterhout, Cock van; Grigoriev, Igor V.

2017-01-01

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.

Modeling of diatomic molecule using the Morse potential and the Verlet algorithm

Energy Technology Data Exchange (ETDEWEB)

Fidiani, Elok [Department of Physics, Parahyangan Catholic University, Bandung-Jawa Barat (Indonesia)

2016-03-11

Performing molecular modeling usually uses special software for Molecular Dynamics (MD) such as: GROMACS, NAMD, JMOL etc. Molecular dynamics is a computational method to calculate the time dependent behavior of a molecular system. In this work, MATLAB was used as numerical method for a simple modeling of some diatomic molecules: HCl, H{sub 2} and O{sub 2}. MATLAB is a matrix based numerical software, in order to do numerical analysis, all the functions and equations describing properties of atoms and molecules must be developed manually in MATLAB. In this work, a Morse potential was generated to describe the bond interaction between the two atoms. In order to analyze the simultaneous motion of molecules, the Verlet Algorithm derived from Newton’s Equations of Motion (classical mechanics) was operated. Both the Morse potential and the Verlet algorithm were integrated using MATLAB to derive physical properties and the trajectory of the molecules. The data computed by MATLAB is always in the form of a matrix. To visualize it, Visualized Molecular Dynamics (VMD) was performed. Such method is useful for development and testing some types of interaction on a molecular scale. Besides, this can be very helpful for describing some basic principles of molecular interaction for educational purposes.

Modeling of diatomic molecule using the Morse potential and the Verlet algorithm

International Nuclear Information System (INIS)

Fidiani, Elok

2016-01-01

Performing molecular modeling usually uses special software for Molecular Dynamics (MD) such as: GROMACS, NAMD, JMOL etc. Molecular dynamics is a computational method to calculate the time dependent behavior of a molecular system. In this work, MATLAB was used as numerical method for a simple modeling of some diatomic molecules: HCl, H_2 and O_2. MATLAB is a matrix based numerical software, in order to do numerical analysis, all the functions and equations describing properties of atoms and molecules must be developed manually in MATLAB. In this work, a Morse potential was generated to describe the bond interaction between the two atoms. In order to analyze the simultaneous motion of molecules, the Verlet Algorithm derived from Newton’s Equations of Motion (classical mechanics) was operated. Both the Morse potential and the Verlet algorithm were integrated using MATLAB to derive physical properties and the trajectory of the molecules. The data computed by MATLAB is always in the form of a matrix. To visualize it, Visualized Molecular Dynamics (VMD) was performed. Such method is useful for development and testing some types of interaction on a molecular scale. Besides, this can be very helpful for describing some basic principles of molecular interaction for educational purposes.

Epiphytic Diatoms along Environmental Gradients in Western European Shallow Lakes

NARCIS (Netherlands)

Blanco, Saul; Cejudo-Figueiras, Cristina; Alvarez-Blanco, Irene; van Donk, Ellen|info:eu-repo/dai/nl/069838593; Gross, Elisabeth M.; Hansson, Lars-Anders; Irvine, Kenneth; Jeppesen, Erik; Kairesalo, Timo; Moss, Brian; Noges, Tiina; Becares, Eloy

Diatom-based assays have been successfully associated worldwide with the tropic status of lakes. Several studies have demonstrated a correlation between epiphytic diatoms and nutrient load in shallow lakes and wetlands. We examine the relative importance of environmental factors in explaining the

Suggestions for diatom-based monitoring in intermittent streams

Directory of Open Access Journals (Sweden)

Falasco Elisa

2016-01-01

Full Text Available Over the last decades, river lentification processes and droughts have been dramatically spreading worldwide, due to global and local drastic changes due to human activities. Under this scenario, the evaluation of physical disturbance caused by intermittency and droughts has become more and more relevant. In this research, we compare samples collected in Mediterranean streams following both traditional and experimental approaches with the aim of understanding if diatom indices calculated from a new sampling strategy could provide additional information for the physical disturbance assessment. Moreover, we also evaluated the response of functional metrics. Our results demonstrated that even though an enhanced sampling method better reflects hydrological disturbance than the traditional one, diatom indices do not detect it. Conversely, functional traits proved to be important metrics for the hydrological disturbance assessment. In particular, benthic diatom chlorophyll a showed significantly lower values in sections more subject to droughts. With respect to ecological guilds, the motile taxa proved to be linked to depositional areas, which resulted important microhabitats (MHs to be explored in rivers affected by lentification. Including different MHs in the sampling process improves the information we can obtain from the analysis of the diatom community and presents important implications in documenting species distribution and autecology.

Unexpected mobility of OH+ and OD+ molecular ions in cooled helium gas

International Nuclear Information System (INIS)

Isawa, R; Yamazoe, J; Tanuma, H; Ohtsuki, K

2012-01-01

Mobilities of OH + and OD + ions in cooled helium gas have been measured at gas temperature of 4.3 K. Measured mobilities of both ions as a function of an effective temperature T eff show a minimum around 80 K, and they are approaching to the polarization limits at very low T eff . These findings will be related to the extremely strong anisotropy of the interaction potential between the molecular ion and helium atom.

Environmental and Spatial Influences on Biogeography and Community Structure of Benthic Diatoms

Science.gov (United States)

Plante, C.; Hill-Spanik, K.; Lowry, J.

2016-02-01

Several theoretical and practical reasons suggest that benthic microalgae could be useful bioindicators. For instance, an ideal indicator species or community would be associated with a given habitat due to local physical conditions or biotic interactions (i.e., `environmental filtering'), not due to dispersal limitation. Due to their small size, immense abundances, and reliance on passive dispersal, the popular notion about micro-organisms is that `Everything is everywhere, but, the environment selects' (Baas-Becking 1934). Although much recent research concerning planktonic bacteria and dispersal limitation has been conducted, very little in this regard is known about microeukaryotes, especially benthic microbes. The purpose of our study was to identify and compare spatial and environmental influences on benthic diatom community structure and biogeography. In summer 2015, sediment was sampled at various spatial scales from four barrier island beaches in South Carolina, USA, and high-throughput (Ion Torrent) DNA sequencing was used to characterize diatom assemblages. ANOSIM and principal coordinates analysis revealed that communities were statistically distinct on the four islands. Community dissimilarity was compared to both spatial distance and environmental differences to determine potential influences of these variables on community structure. We found that geographic distance had the strongest correlation with community similarity, with and without one anomalous location, while differences in temperature (air, water, and sediment), nutrients, organic matter, and turbidity also had significant but weaker relationships with community structure. Surprisingly, air temperature, which changes on very short time scales, appeared to be the environmental factor most strongly related to diatom species composition, potentially implicating some unmeasured variable (e.g., cloud cover). However, we also found that temperature and geographic distance were strongly

Theoretical study of the electronic structure of different states of the KRb+ molecular ion

International Nuclear Information System (INIS)

Korek, M.; Younis, G.

2000-01-01

Full text.The molecular activities in ultra-cold alkali atom trapping stimulate theoretical developments to compute relevant adiabatic potential curves, especially in the framework of the pseudopotential methods. For these methods the molecular ion KRb+ is treated as system with one active electron moving in a field of two ionic cores, where core valence electron interactions are presented by an effective potential. Potential energies have been calculated over a wide range of internuclear distance (5.0-60a o ) for the lowest states of symmetry 2 Σ, 2 Π, 2 Δ and Ω for the molecular ion KRb+. To avoid an over estimation of the dissociation energy the perturbative treatment is replaced by an l-dependent core-polarization potential of the Foucrault et al. For the one valence electron of the two considered atoms, we recalculated the polarization potential cut-off parameters r k l , and r R b l by taking l=0,1,2 and r i 2 =r i 3 . Molecular orbital for the molecular ion KRb+ were derived from Self Consistent Field calculations (SCF), and full valence Configuration Interaction (IC) calculations were performed. Extensive tables of energy values versus internuclear distance are displayed and molecular spectroscopic constants have been derived, for the first time, for the bound states with regular shape

Thermal characterization of Ag and Ag + N ion implanted ultra-high molecular weight polyethylene (UHMWPE)

Energy Technology Data Exchange (ETDEWEB)

Sokullu Urkac, E. [Department of Materials Science, Izmir High Technology Institute, Gulbahcekoyu Urla, Izmir (Turkey)]. E-mail: emelsu@gmail.com; Oztarhan, A. [Bioengineering Department, Ege University, Bornova, Izmir 35100 (Turkey); Tihminlioglu, F. [Department of Chemical Engineering, Izmir High Technology Institute, Gulbahcekoyu Urla, Izmir (Turkey); Kaya, N. [Bioengineering Department, Ege University, Bornova, Izmir 35100 (Turkey); Ila, D. [Center for Irradiation of Materials, Alabama A and M University, Normal AL 35762 (United States); Muntele, C. [Center for Irradiation of Materials, Alabama A and M University, Normal AL 35762 (United States); Budak, S. [Center for Irradiation of Materials, Alabama A and M University, Normal AL 35762 (United States); Oks, E. [H C Electronics Institute, Tomsk (Russian Federation); Nikolaev, A. [H C Electronics Institute, Tomsk (Russian Federation); Ezdesir, A. [R and D Department, PETKIM Holding A.S., Aliaga, Izmir 35801 (Turkey); Tek, Z. [Department of Physics, Celal Bayar University, Manisa (Turkey)

2007-08-15

Most of total hip joints are composed of ultra-high molecular weight polyethylene (UHMWPE ). However, as ultra-high molecular weight polyethylene is too stable in a body, wear debris may accumulate and cause biological response such as bone absorption and loosening of prosthesis. In this study, ultra-high molecular weight polyethylene samples were Ag and Ag + N hybrid ion implanted by using MEVVA ion implantation technique to improve its surface properties. Samples were implanted with a fluence of 10{sup 17} ion/cm{sup 2} and extraction voltage of 30 kV. Implanted and unimplanted samples were investigated by thermo-gravimetry analysis (TGA), differential scanning calorimetry (DSC), X-ray diffraction (XRD) analysis, scanning electron microscopy (SEM), optical microscopy (OM) and contact Angle measurement. Thermal characterization results showed that the ion bombardment induced an increase in the % crystallinity, onset and termination degradation temperatures of UHMWPE.

Discovery of energetic molecular ions (NO+ and O2+) in the storm time ring current

International Nuclear Information System (INIS)

Klecker, B.; Moebius, E.; Hovestadt, D.; Scholer, M.; Gloeckler, G.; Ipavich, F.M.

1986-01-01

A few hours after the onset of a large geomagnetic storm on September 4, 1984, energetic molecular ions in the mass range 28--32, predminantly NO + and O 2 + , have been discovered in the outer ring current at L--7. The data have been obtained with the time-of-flight spectrometer SULEICA on the AMPTE/IRM spacecraft. We find at 160 keV/e a mean abundance ratio of the molecular ions relative to O + ions of 0.031 +- 0.004. During quiet times no molecular ions are observed, the 1 sigma upper limit of the ratio derived by averaging over several quiet periods is 0.003. The observations demonstrate the injection of ionospheric plasma into the storm time ring current and the subsequent acceleration to energies of several hundred keV on a time scale of a few hours after the onset of the magnetic storm

Cenozoic planktonic marine diatom diversity and correlation to climate change.

Directory of Open Access Journals (Sweden)

David Lazarus

Full Text Available Marine planktonic diatoms export carbon to the deep ocean, playing a key role in the global carbon cycle. Although commonly thought to have diversified over the Cenozoic as global oceans cooled, only two conflicting quantitative reconstructions exist, both from the Neptune deep-sea microfossil occurrences database. Total diversity shows Cenozoic increase but is sample size biased; conventional subsampling shows little net change. We calculate diversity from a separately compiled new diatom species range catalog, and recalculate Neptune subsampled-in-bin diversity using new methods to correct for increasing Cenozoic geographic endemism and decreasing Cenozoic evenness. We find coherent, substantial Cenozoic diversification in both datasets. Many living cold water species, including species important for export productivity, originate only in the latest Miocene or younger. We make a first quantitative comparison of diatom diversity to the global Cenozoic benthic ∂(18O (climate and carbon cycle records (∂(13C, and 20-0 Ma pCO2. Warmer climates are strongly correlated with lower diatom diversity (raw: rho = .92, p.9, detrended r>.6, all p<.001, but only weakly over the earlier Cenozoic, suggesting increasingly strong linkage of diatom and climate evolution in the Neogene. Our results suggest that many living marine planktonic diatom species may be at risk of extinction in future warm oceans, with an unknown but potentially substantial negative impact on the ocean biologic pump and oceanic carbon sequestration. We cannot however extrapolate our my-scale correlations with generic climate proxies to anthropogenic time-scales of warming without additional species-specific information on proximate ecologic controls.

Resonant inelastic collisions of electrons with diatomic molecules

International Nuclear Information System (INIS)

Houfek, Karel

2012-01-01

In this contribution we give a review of applications of the nonlocal resonance theory which has been successfully used for treating the nuclear dynamics of low-energy electron collisions with diatomic molecules over several decades. We give examples and brief explanations of various structures observed in the cross sections of vibrational excitation and dissociative electron attachment to diatomic molecules such as threshold peaks, boomerang oscillations below the dissociative attachment threshold, or outer-well resonances.

Resonant inelastic collisions of electrons with diatomic molecules

Energy Technology Data Exchange (ETDEWEB)

Houfek, Karel, E-mail: karel.houfek@gmail.com [Institute of Theoretical Physics, Faculty of Mathematics and Physics, Charles University, V Holesovickach 2, 180 00 Prague 8 (Czech Republic)

2012-05-15

In this contribution we give a review of applications of the nonlocal resonance theory which has been successfully used for treating the nuclear dynamics of low-energy electron collisions with diatomic molecules over several decades. We give examples and brief explanations of various structures observed in the cross sections of vibrational excitation and dissociative electron attachment to diatomic molecules such as threshold peaks, boomerang oscillations below the dissociative attachment threshold, or outer-well resonances.

Toxicity of dissolved and precipitated aluminium to marine diatoms.

Science.gov (United States)

Gillmore, Megan L; Golding, Lisa A; Angel, Brad M; Adams, Merrin S; Jolley, Dianne F

2016-05-01

Localised aluminium contamination can lead to high concentrations in coastal waters, which have the potential for adverse effects on aquatic organisms. This research investigated the toxicity of 72-h exposures of aluminium to three marine diatoms (Ceratoneis closterium (formerly Nitzschia closterium), Minutocellus polymorphus and Phaeodactylum tricornutum) by measuring population growth rate inhibition and cell membrane damage (SYTOX Green) as endpoints. Toxicity was correlated to the time-averaged concentrations of different aluminium size-fractions, operationally defined as aluminium exposure varied between diatom species. C. closterium was the most sensitive species (10% inhibition of growth rate (72-h IC10) of 80 (55-100)μg Al/L (95% confidence limits)) while M. polymorphus (540 (460-600)μg Al/L) and P. tricornutum (2100 (2000-2200)μg Al/L) were less sensitive (based on measured total aluminium). Dissolved aluminium was the primary contributor to toxicity in C. closterium, while a combination of dissolved and precipitated aluminium forms contributed to toxicity in M. polymorphus. In contrast, aluminium toxicity to the most tolerant diatom P. tricornutum was due predominantly to precipitated aluminium. Preliminary investigations revealed the sensitivity of C. closterium and M. polymorphus to aluminium was influenced by initial cell density with aluminium toxicity significantly (paluminium toxicity to diatoms do not involve compromising the plasma membrane. These results indicate that marine diatoms have a broad range in sensitivity to aluminium with toxic mechanisms related to both dissolved and precipitated aluminium. Copyright © 2016 Elsevier B.V. All rights reserved.

Spectral radiation dependent photoprotective mechanism in the diatom Pseudo-nitzschia multistriata.

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Christophe Brunet

Full Text Available Phytoplankton, such as diatoms, experience great variations of photon flux density (PFD and light spectrum along the marine water column. Diatoms have developed some rapidly-regulated photoprotective mechanisms, such as the xanthophyll cycle activation (XC and the non-photochemical chlorophyll fluorescence quenching (NPQ, to protect themselves from photooxidative damages caused by excess PFD. In this study, we investigate the role of blue fluence rate in combination with red radiation in shaping photoacclimative and protective responses in the coastal diatom Pseudo-nitzschia multistriata. This diatom was acclimated to four spectral light conditions (blue, red, blue-red, blue-red-green, each of them provided with low and high PFD. Our results reveal that the increase in the XC pool size and the amplitude of NPQ is determined by the blue fluence rate experienced by cells, while cells require sensing red radiation to allow the development of these processes. Variations in the light spectrum and in the blue versus red radiation modulate either the photoprotective capacity, such as the activation of the diadinoxanthin-diatoxanthin xanthophyll cycle, the diadinoxanthin de-epoxidation rate and the capacity of non-photochemical quenching, or the pigment composition of this diatom. We propose that spectral composition of light has a key role on the ability of diatoms to finely balance light harvesting and photoprotective capacity.

Tinted windows: The presence of the UV absorbing compounds called mycosporine-like amino acids embedded in the frustules of marine diatoms

Science.gov (United States)

Ingalls, Anitra E.; Whitehead, Kenia; Bridoux, Maxime C.

2010-01-01

Diatom frustule-bound organic compounds presumably play an important role in biomineralization and constitute an important pool of organic matter preserved in diatom frustule-rich sediments. In this study, detailed analysis of diatom frustule-bound organic matter in opal-rich Southern Ocean plankton and sediments revealed for the first time the presence of low molecular weight, UV light absorbing compounds called mycosporine-like amino acids (MAAs). Chemically cleaned diatom frustule-derived biosilica was dissolved in HF, releasing bound or entrapped organic compounds that were subsequently characterized using liquid chromatography with UV-Vis and electrospray ionization mass spectrometry (LC/PDA/ESI-MS). Palythine ([M+H] + = 245), porphyra-334 ([M+H] + = 347) and shinorine ([M+H] + = 333) were the most abundant MAAs detected in HF digests of plankton and sediment. Traces of asterina ([M+H] + = 289), palythinol ([M+H] + = 303) and palythinic acid ([M+H] + = 329) were also detected. MAAs in cleaned HF digested frustules were up to two orders of magnitude more abundant than methanol extractable MAAs. MAAs are substituted with acid hydrolysable amino acid residues. Our results suggest that MAAs, and not proteins, could be responsible for the high proportion of the amino acids glycine and threonine found in hydrolysates of HF digested diatom-rich environmental samples. Total MAAs accounted for 3-27% of the carbon and 2-18% of total nitrogen in the frustules undergoing various chemical cleaning treatments. This is the first report of MAAs in close association with a mineral phase and we hypothesize that the mineral matrix could stabilize these compounds, thereby enhancing photoprotection against the harmful effects of UV light. The presence of frustule-bound MAAs in sediment cores further suggests the possibility that they could be used in compound-specific isotope analysis of diatom-bound organic matter and as indicators of past solar irradiance.

Whole-cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum.

Science.gov (United States)

Alipanah, Leila; Rohloff, Jens; Winge, Per; Bones, Atle M; Brembu, Tore

2015-10-01

Algal growth is strongly affected by nitrogen (N) availability. Diatoms, an ecologically important group of unicellular algae, have evolved several acclimation mechanisms to cope with N deprivation. In this study, we integrated physiological data with transcriptional and metabolite data to reveal molecular and metabolic modifications in N-deprived conditions in the marine diatom Phaeodactylum tricornutum. Physiological and metabolite measurements indicated that the photosynthetic capacity and chlorophyll content of the cells decreased, while neutral lipids increased in N-deprived cultures. Global gene expression analysis showed that P. tricornutum responded to N deprivation through an increase in N transport, assimilation, and utilization of organic N resources. Following N deprivation, reduced biosynthesis and increased recycling of N compounds like amino acids, proteins, and nucleic acids was observed at the transcript level. The majority of the genes associated with photosynthesis and chlorophyll biosynthesis were also repressed. Carbon metabolism was restructured through downregulation of the Calvin cycle and chrysolaminarin biosynthesis, and co-ordinated upregulation of glycolysis, the tricarboxylic acid cycle, and pyruvate metabolism, leading to funnelling of carbon sources to lipid metabolism. Finally, reallocation of membrane lipids and induction of de novo triacylglycerol biosynthesis directed cells to accumulation of neutral lipids. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Molecular projectile effects for kinetic electron emission from carbon- and metal-surfaces bombarded by slow hydrogen ions

International Nuclear Information System (INIS)

Cernusca, S.; Winter, H.P.; Aumayr, F.; Diez Muino, R.; Juaristi, J.I.

2003-01-01

Total yields for kinetic electron emission (KE) have been determined for impact of hydrogen monomer-, dimer- and trimer-ions (impact energy <10 keV) on atomically clean surfaces of carbon-fiber inforced graphite used as first-wall armour in magnetic fusion devices. The data are compared with KE yields for impact of same projectile ions on atomically clean highly oriented pyrolytic graphite and polycrystalline gold. We discuss KE yields for the different targets if bombarded by equally fast molecular and atomic ions in view to 'projectile molecular effects' (different yields per proton for equally fast atomic and molecular ions), which are expected from calculated electronic projectile energy losses in these target materials

Molecular projectile effects for kinetic electron emission from carbon- and metal-surfaces bombarded by slow hydrogen ions

CERN Document Server

Cernusca, S; Aumayr, F; Diez-Muino, R; Juaristi, J I

2003-01-01

Total yields for kinetic electron emission (KE) have been determined for impact of hydrogen monomer-, dimer- and trimer-ions (impact energy <10 keV) on atomically clean surfaces of carbon-fiber inforced graphite used as first-wall armour in magnetic fusion devices. The data are compared with KE yields for impact of same projectile ions on atomically clean highly oriented pyrolytic graphite and polycrystalline gold. We discuss KE yields for the different targets if bombarded by equally fast molecular and atomic ions in view to 'projectile molecular effects' (different yields per proton for equally fast atomic and molecular ions), which are expected from calculated electronic projectile energy losses in these target materials.

The application and testing of diatom-based indices of stream water ...

African Journals Online (AJOL)

The application and testing of diatom-based indices of stream water quality in Chinhoyi Town, Zimbabwe. ... PROMOTING ACCESS TO AFRICAN RESEARCH ... test the applicability of foreign diatom-based water quality assessment indices to ...

Recent advances in biological effect and molecular mechanism of arabidopsis thaliana irradiated by ion beams

International Nuclear Information System (INIS)

Wu Dali; Hou Suiwen; Li Wenjian

2008-01-01

Newly research progresses were summarized in effect of ion beams on seed surface, biological effect, growth, development, gravitropism and so on. Furthermore, mutation molecular mechanism of Arabidopsis thaliana was discussed, for example, alteration of DNA bases, DNA damage, chromosomal recombination, characteristics of mutant transmissibility, etc. Meanwhile, the achievements of transfer- ring extraneous gene to Arabidopsis thaliana by ion beams were reviewed in the paper. At last, the future prospective are also discussed here in mutation molecular mechanism and the potential application of biological effect of heavy ion beams. (authors)

Diatom species composition in the Raška river (Southwestern Serbia

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Vidaković Danijela P.

2015-01-01

Full Text Available The paper presents data on the composition of epilithic diatoms in the Raška River. Samples were collected by scraping stone surfaces with a brush from 5 localities along the Raška River in April, June, August and November 2011 and March and May 2012. Diatom frustules were cleaned using cold acid method, and mounted on permanent slides. An investigation of the Raška River resulted in description of 106 diatom taxa. The most species rich genera are Navicula (10, Gomphonema (10 and Nitzschia (9, while other genera are presented with one or more species. Detailed floristic analysis of the benthic diatom flora in this river has not been conducted before. Therefore, this paper provides a groundwork for future researches. [Projekat Ministarstva nauke Republike Srbije, br. TR 037009

On the theory of a dissociative recombination of electrons and molecular ions

International Nuclear Information System (INIS)

Golubkov, G.V.; Drygin, S.V.; Ivanov, G.K.

1995-01-01

The present paper deals with a detailed description of molecular recombination of the electron and two-atom molecular ion, as well as with consideration of the this complex quantum-mechanical process. It is shown that this relationship results in a displacement of vibrational resonance levels and deformation of line contour

Secondary electron emission from Au by medium energy atomic and molecular ions

CERN Document Server

Itoh, A; Obata, F; Hamamoto, Y; Yogo, A

2002-01-01

Number distributions of secondary electrons emitted from a Au metal surface have been measured for atomic and molecular ions of H sup + , He sup + , C sup + , N sup + , O sup + , H sup + sub 2 , H sup + sub 3 , HeH sup + , CO sup + and O sup + sub 2 in the energy range 0.3-2.0 MeV. The emission statistics obtained are described fairly well by a Polya function. The Polya parameter b, determining the distribution shape, is found to decrease monotonously with increasing emission yield gamma, revealing a surprising relationship of b gamma approx 1 over the different projectile species and impact energies. This finding supports certainly the electron cascading model. Also we find a strong negative molecular effect for heavier molecular ions, showing a significant reduction of gamma compared to the estimated values using constituent atomic projectile data.

Bioactive glass 45S5 from diatom biosilica

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Luqman A. Adams

2017-12-01

Full Text Available A major draw-back to large scale production of bioactive glasses is the high cost of the standard silica precursor, usually tetraethyl orthosilicate (TEOS. The current study describes a novel sol–gel preparation of 45S5 bioactive glass using diatom biosilica from cultured cells of the diatom, Aulacoseira granulata as substitute to TEOS. The glass formed was characterized using mechanical tester, scanning electron microscopy (SEM, energy dispersive X-ray analysis (EDX, X-ray diffraction (XRD and Fourier transform infrared (FTIR spectroscopy. Results showed that the glass possessed a compressive strength of 3.75 ± 0.18 and formed carbonated hydroxyapatite (HCA within 7 days in simulated body fluid (SBF, attributable to good surface chemistry. The performance of the glass was compared with that of those formed using TEOS. Diatom biosilica could be a potential economically friendly starting material for large scale fabrication of bioactive glasses.

The molecular mechanism of multi-ion conduction in K{sup +} channels

Energy Technology Data Exchange (ETDEWEB)

Gwan, J.F.

2007-01-19

Steered molecular dynamics (SMD) simulation method is applied to a fully solvated membrane-channel model for studying the ion permeation process in potassium channels. The channel model is based on the crystallographic structure of a prokaryotic K{sup +} channel- the KcsA channel, which is a representative of most known eukaryotic K{sup +} channels. It has long been proposed that the ion transportation in a conventional K{sup +}-channel follows a multi-ion fashion: permeating ions line in a queue in the channel pore and move in a single file through the channel. The conventional view of multi-ion transportation is that the electrostatic repulsion between ions helps to overcome the attraction between ions and the channel pore. In this study, we proposed two SMD simulation schemes, referred to 'the single-ion SMD' simulations and 'the multi-ion SMD' simulations. Concerted movements of a K-W-K sequence in the selectivity filter were observed in the single-ion SMD simulations. The analysis of the concerted movement reveals the molecular mechanism of the multi-ion transportation. It shows that, rather than the long range electrostatic interaction, the short range polar interaction is a more dominant factor in the multi-ion transportation. The polar groups which play a role in the concerted transportation are the water molecules and the backbone carbonyl groups of the selectivity filter. The polar interaction is sensitive to the relative orientation of the polar groups. By changing the orientation of a polar group, the interaction may switch from attractive to repulsive or vice versa. By this means, the energy barrier between binding sites in the selectivity filter can be switched on and off, and therefore the K{sup +} may be able to move to the neighboring binding site without an external driving force. The concerted transportation in the selectivity filter requires a delicate cooperation between K{sup +}, waters, and the backbone carbonyl groups. To

Intensive aggregate formation with low vertical flux during an upwelling-induced diatom bloom

DEFF Research Database (Denmark)

Kiørboe, Thomas; Tiselius, P.; Mitchell-Innes, B.

1998-01-01

of turbulent shear in the ocean such stickiness coefficients predict very high specific coagulation rates (0.3 d(-1)). In situ video observation demonstrated the occurrence of abundant diatom aggregates with surface water concentrations between 1,000 and 3,000 ppm. Despite the very high concentration......The surfaces of most pelagic diatoms are sticky at times and may therefore form rapidly settling aggregates by physical coagulation. Stickiness and aggregate formation may be particularly adaptive in upwelling systems by allowing the retention of diatom populations in the vicinity of the upwelling...... center. We therefore hypothesized that upwelling diatom blooms are terminated by aggregate formation and rapid sedimentation. We monitored the development of a maturing diatom (mainly Chaetoceros spp.) bloom in the Benguela upwelling current during 7 d in February. Chlorophyll concentrations remained...

Evolutionary origins and functions of the carotenoid biosynthetic pathway in marine diatoms.

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Sacha Coesel

Full Text Available Carotenoids are produced by all photosynthetic organisms, where they play essential roles in light harvesting and photoprotection. The carotenoid biosynthetic pathway of diatoms is largely unstudied, but is of particular interest because these organisms have a very different evolutionary history with respect to the Plantae and are thought to be derived from an ancient secondary endosymbiosis between heterotrophic and autotrophic eukaryotes. Furthermore, diatoms have an additional xanthophyll-based cycle for dissipating excess light energy with respect to green algae and higher plants. To explore the origins and functions of the carotenoid pathway in diatoms we searched for genes encoding pathway components in the recently completed genome sequences of two marine diatoms. Consistent with the supplemental xanthophyll cycle in diatoms, we found more copies of the genes encoding violaxanthin de-epoxidase (VDE and zeaxanthin epoxidase (ZEP enzymes compared with other photosynthetic eukaryotes. However, the similarity of these enzymes with those of higher plants indicates that they had very probably diversified before the secondary endosymbiosis had occurred, implying that VDE and ZEP represent early eukaryotic innovations in the Plantae. Consequently, the diatom chromist lineage likely obtained all paralogues of ZEP and VDE genes during the process of secondary endosymbiosis by gene transfer from the nucleus of the algal endosymbiont to the host nucleus. Furthermore, the presence of a ZEP gene in Tetrahymena thermophila provides the first evidence for a secondary plastid gene encoded in a heterotrophic ciliate, providing support for the chromalveolate hypothesis. Protein domain structures and expression analyses in the pennate diatom Phaeodactylum tricornutum indicate diverse roles for the different ZEP and VDE isoforms and demonstrate that they are differentially regulated by light. These studies therefore reveal the ancient origins of several

Evolutionary origins and functions of the carotenoid biosynthetic pathway in marine diatoms.

Science.gov (United States)

Coesel, Sacha; Oborník, Miroslav; Varela, Joao; Falciatore, Angela; Bowler, Chris

2008-08-06

Carotenoids are produced by all photosynthetic organisms, where they play essential roles in light harvesting and photoprotection. The carotenoid biosynthetic pathway of diatoms is largely unstudied, but is of particular interest because these organisms have a very different evolutionary history with respect to the Plantae and are thought to be derived from an ancient secondary endosymbiosis between heterotrophic and autotrophic eukaryotes. Furthermore, diatoms have an additional xanthophyll-based cycle for dissipating excess light energy with respect to green algae and higher plants. To explore the origins and functions of the carotenoid pathway in diatoms we searched for genes encoding pathway components in the recently completed genome sequences of two marine diatoms. Consistent with the supplemental xanthophyll cycle in diatoms, we found more copies of the genes encoding violaxanthin de-epoxidase (VDE) and zeaxanthin epoxidase (ZEP) enzymes compared with other photosynthetic eukaryotes. However, the similarity of these enzymes with those of higher plants indicates that they had very probably diversified before the secondary endosymbiosis had occurred, implying that VDE and ZEP represent early eukaryotic innovations in the Plantae. Consequently, the diatom chromist lineage likely obtained all paralogues of ZEP and VDE genes during the process of secondary endosymbiosis by gene transfer from the nucleus of the algal endosymbiont to the host nucleus. Furthermore, the presence of a ZEP gene in Tetrahymena thermophila provides the first evidence for a secondary plastid gene encoded in a heterotrophic ciliate, providing support for the chromalveolate hypothesis. Protein domain structures and expression analyses in the pennate diatom Phaeodactylum tricornutum indicate diverse roles for the different ZEP and VDE isoforms and demonstrate that they are differentially regulated by light. These studies therefore reveal the ancient origins of several components of the

Simulation of the energy spectra of original versus recombined H2+ molecular ions transmitted through thin foils

International Nuclear Information System (INIS)

Barriga-Carrasco, Manuel D.; Garcia-Molina, Rafael

2004-01-01

This work presents the results of computer simulations for the energy spectra of original versus recombined H 2 + molecular ions transmitted through thin amorphous carbon foils, for a broad range of incident energies. A detailed description of the projectile motion through the target has been done, including nuclear scattering and Coulomb repulsion as well as electronic self-retarding and wake forces; the two latter are calculated in the dielectric formalism framework. Differences in the energy spectra of recombined and original transmitted H 2 + molecular ions clearly appear in the simulations, in agreement with the available experimental data. Our simulation code also differentiates the contributions due to original and to recombined H 2 + molecular ions when the energy spectra contain both contributions, a feature that could be used for experimental purposes in estimating the ratio between the number of original and recombined H 2 + molecular ions transmitted through thin foils

Diatoms as an indicator for tile drainage flow in a German lowland catchment.

Science.gov (United States)

Wu, Naicheng; Faber, Claas; Ulrich, Uta; Fohrer, Nicola

2018-01-01

The separation of runoff components within a model simulation is of great importance for a successful implementation of management measures. Diatoms could be a promising indicator for tile drainage flow due to their diverse preferences to different aquatic habitats. In this study, we collected diatom samples of 9 sites (4 tile drainage, TD, and 5 river sites, Ri) in a German lowland catchment at a weekly or biweekly time step from March to July 2013 with the aim of testing the suitability of diatoms for tile drainage flow, which is typical for lowland catchment. Planothidium lanceolatum , Ulnaria biceps , and Navicula gregaria dominated in TD sites with relative abundances of 22.2, 21.5, and 10.9%, respectively. For Ri sites, the most abundant species was Navicula lanceolata (20.5%), followed by Ulnaria biceps (12.9%), Cyclotella meneghiniana (9.5%), and Planothidium lanceolatum (9.3%). Compared with Ri sites, TD had a lower diatom density, biomass, species richness, and percentage of Aquatic/Riparian diatoms (AqRi%). However, the proportion of Riparian diatoms (RiZo%) increased at TD. Indicator value method (IndVal) revealed that the two groups (Ri and TD) were characterized by different indicator species. Fifteen taxa, including Cocconeis placentula , Cyclotella meneghiniana , N. lanceolata , and U. biceps , were significant indicators for Ri sites. Planothidium lanceolatum , Achnanthidium minutissimum , and Navicula gregaria were significant indicators for TD sites. A pronounced variation was found in the species lists of diatom community between Ri and TD water body types associated with different indicator species. With respect to hydrograph separation, these findings highlight the suitability of diatoms as an indicator for tile drainage flow. However, spatial and temporal variations of diatoms should be considered in future surveys.

Atomistic simulation of damage production by atomic and molecular ion irradiation in GaN

International Nuclear Information System (INIS)

Ullah, M. W.; Kuronen, A.; Nordlund, K.; Djurabekova, F.; Karaseov, P. A.; Titov, A. I.

2012-01-01

We have studied defect production during single atomic and molecular ion irradiation having an energy of 50 eV/amu in GaN by molecular dynamics simulations. Enhanced defect recombination is found in GaN, in accordance with experimental data. Instantaneous damage shows non-linearity with different molecular projectile and increasing molecular mass. Number of instantaneous defects produced by the PF 4 molecule close to target surface is four times higher than that for PF 2 molecule and three times higher than that calculated as a sum of the damage produced by one P and four F ion irradiation (P+4×F). We explain this non-linearity by energy spike due to molecular effects. On the contrary, final damage created by PF 4 and PF 2 shows a linear pattern when the sample cools down. Total numbers of defects produced by Ag and PF 4 having similar atomic masses are comparable. However, defect-depth distributions produced by these species are quite different, also indicating molecular effect.

Getting the ion-protein interactions right in molecular dynamics simulations

Czech Academy of Sciences Publication Activity Database

Duboué-Dijon, Elise; Mason, Philip E.; Jungwirth, Pavel

2017-01-01

Roč. 46, Suppl 1 (2017), S66 ISSN 0175-7571. [IUPAB congress /19./ and EBSA congress /11./. 16.07.2017-20.07.2017, Edinburgh] Institutional support: RVO:61388963 Keywords : ion-protein interaction * molecular dynamics simulations * neutron scattering * insulin Subject RIV: BO - Biophysics

The relevance of diatoms for water quality assessment in South ...

African Journals Online (AJOL)

Water quality assessment protocols based on the use of diatoms are now well developed and their value substantiated at an international level. The use of diatoms is not designed or intended to be a “rapid” technology. The detailed level of information generated from the procedure outweighs perceived disadvantages of ...

Diatom assemblage in a tropical lake of northeastern Brazil

Directory of Open Access Journals (Sweden)

Lilian Rodrigues do Nascimento

2010-02-01

Full Text Available The composition and spatial variation of diatom assemblage in surface sediments of Caçó Lake (shallow, mesotrophic and weakly acid lake - Maranhão State, Brazil were analyzed in order to know the distribution pattern of the species along the lake during rainy season (April 1999. Four zones were established in the lake based on 21 diatoms species and habitat affinities. The first three zones (prime three meters deep to six meters deep were marked by the occurrence of Pinnularia gigas, Frustulia rhomboides, Encyonopsis krasskei, Eunotia camelus, E. femoriformis and E. monodon. Zone IV (seven to nine meters deep was inhabited mainly by Surirella biseriata and Fragilariforma floridana. During the beginning of the rainy season, the diatom assemblage in Caçó Lake was composed mainly by benthic and epiphytic forms that reflected the low lake levels and the abundance of littoral vegetation present in this lake.Com o objetivo de se conhecer a dinâmica espacial e a distribuição das diatomáceas contidas no sedimento superficial do lago Caçó, durante o período de chuvas (abril de 1999 foram realizadas coletas em um "transect" horizontal. A partir da observação destas coletas efetuadas a cada 1 metro pode-se observar que a distribuição das diatomáceas esteve fortemente ligada a ocorrência do banco de macrófitas da sua margem, com a ocorrência maciça das espécies epifíticas e bentônicas. A análise de agrupamento de dados permitiu uma melhor visualização, da sua distribuição a cada profundidade e também das associações específicas em cada zona. Os resultados deste estudo permitiram concluir que a ocorrência e distribuição das diatomáceas do Lago Caçó está fortemente ligada ao banco de macrófitas localizado em suas margens, definindo assim zonas características dentro do lago.

Biological monitoring of lotic ecosystems: the role of diatoms Biomonitoramento dos ecossistemas lóticos: o papel das diatomáceas

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T. Bere

2010-08-01

Full Text Available Increasing anthropogenic influence on lotic environments as a result of civilisation has captured public interest because of the consequent problems associated with deterioration of water quality. Various biological monitoring methods that provide a direct measure of ecological integrity by using the response of biota to environmental changes have been developed to monitor the ecological status of lotic environments. Diatoms have been used extensively in this regard and this review attempts to summarise the basic concepts associated with biological monitoring using benthic diatoms. Where possible, examples from work carried out in Brazil are used.O aumento da influência antropogênica sobre ambientes lóticos como resultado da civilização conquistou o interesse público por causa de problemas relacionados com a consequente deterioração da qualidade da água. Vários métodos de biomonitoramento que fornecem uma medida direta da integridade ecológica usando a resposta da biota a alterações ambientais têm sido desenvolvidos para monitorar o estado ecológico de ecossistemas lóticos. Diatomáceas têm sido amplamente utilizadas e esta revisão tenta resumir os conceitos básicos associados ao monitoramento biológico utilizando diatomáceas bentônicas. Sempre que possível, exemplos de trabalhos realizados no Brasil serão utilizados.

Insights into global diatom distribution and diversity in the world’s ocean

KAUST Repository

Malviya, Shruti; Scalco, Eleonora; Audic, Sté phane; Vincent, Flora; Veluchamy, Alaguraj; Poulain, Julie; Wincker, Patrick; Iudicone, Daniele; de Vargas, Colomban; Bittner, Lucie; Zingone, Adriana; Bowler, Chris

2016-01-01

Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of ∼12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 sizefractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron. We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered.

Insights into global diatom distribution and diversity in the world’s ocean

KAUST Repository

Malviya, Shruti

2016-03-01

Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of ∼12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 sizefractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron. We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered.

Influence of land-use patterns on benthic diatom communities and ...

African Journals Online (AJOL)

The objective of this study was to determine the effects of land-use patterns on both diatom community composition and water quality in tropical streams during the dry season. Benthic diatom collections and water quality sampling were done 4 times at 10 sites. A suite of environmental variables that varied with human ...

Molecular growth in clusters of polycyclic aromatic hydrocarbons induced by collisions with ions

International Nuclear Information System (INIS)

Delaunay, Rudy

2016-01-01

This thesis concerns the experimental study of the interaction between low energy ions (keV range) and neutral isolated molecules or clusters of polycyclic aromatic hydrocarbons (PAH) in the gas phase. The use of ionising radiations on these complex molecular systems of astrophysical interest allowed to highlight processes of statistical fragmentation, corresponding to the redistribution of the energy through the degrees of freedom of the target, and non-statistical fragmentation, linked to binary collisions of the ions on the nuclei of the target. A mechanism of intermolecular growth in clusters of PAH is observed. It is associated to the ultrafast (≤ ps) formation of fragments inside the clusters following binary collisions. The presence of a molecular environment around the fragments formed during the interaction may initiate a process of reactivity between the fragments and the molecules of the clusters. More precisely, the study focusses on the importance of the electronic stopping power SE and the nuclear stopping power SN of the projectile ion. It shows that the molecular growth is enhanced when SN is higher than SE. This can be explained by the fact that the deposit of energy is mainly due to the interaction with the nuclei of the target. The process of growth has been observed for all the molecules of PAH studied during this thesis and also for nitrogenated analogues of the molecule of anthracene. This demonstrates that molecular growth may be efficiently induced by collisions of low energy ions with clusters of PAH. (author) [fr

Sorption of Molecular Oxygen by Metal-Ion Exchanger Nanocomposites

Science.gov (United States)

Krysanov, V. A.; Plotnikova, N. V.; Kravchenko, T. A.

2018-03-01

Kinetic features are studied of the chemisorption and reduction of molecular oxygen from water by metal-ion exchanger nanocomposites that differ in the nature of the dispersed metal and state of oxidation. In the Pd equilibrium sorption coefficient for oxygen dissolved in water ranges from 20 to 50, depending on the nature and oxidation state of the metal component.

Laser Spectroscopy of Ruthenium Containing Diatomic Molecules: RuH/D and RuP.

Science.gov (United States)

Adam, Allan G.; Konder, Ricarda M.; Nickerson, Nicole M.; Linton, Colan; Tokaryk, D. W.

2015-06-01

In the last few years, the Cheung group in Hong Kong and the Steimle group in Arizona have successfully studied several ruthenium containing diatomic molecules, RuX (X =C, O, N, B, using the laser-ablation molecular jet technique. Based on this success, the UNB spectroscopy group decided to try and find the optical signatures of other RuX molecules. Using CH_3OH and PH_3 as reactant gases, the RuH and RuP diatomic molecules have been detected in surveys of the 420 - 675 nm spectral region. RuD has also been made using fully deuterated methanol as a reactant. Dispersed fluorescence experiments have been performed to determine ground state vibrational frequencies and the presence of any low-lying electronic states. Rotationally resolved spectra for these molecules have also been taken and the analysis is proceeding. The most recent results will be presented. F. Wang et al., Journal of Chemical Physics 139, 174318 (2013). N. Wang et al., Journal of Physical Chemistry A 117, 13279 (2013). T. Steimle et al., Journal of Chemical Physics 119, 12965 (2003). N. Wang et al., Chemical Physics Letters 547, 21 (2012).

Cenozoic planktonic marine diatom diversity and correlation to climate change

Science.gov (United States)

Lazarus, David; Barron, John; Renaudie, Johan; Diver, Patrick; Türke, Andreas

2014-01-01

Marine planktonic diatoms export carbon to the deep ocean, playing a key role in the global carbon cycle. Although commonly thought to have diversified over the Cenozoic as global oceans cooled, only two conflicting quantitative reconstructions exist, both from the Neptune deep-sea microfossil occurrences database. Total diversity shows Cenozoic increase but is sample size biased; conventional subsampling shows little net change. We calculate diversity from a separately compiled new diatom species range catalog, and recalculate Neptune subsampled-in-bin diversity using new methods to correct for increasing Cenozoic geographic endemism and decreasing Cenozoic evenness. We find coherent, substantial Cenozoic diversification in both datasets. Many living cold water species, including species important for export productivity, originate only in the latest Miocene or younger. We make a first quantitative comparison of diatom diversity to the global Cenozoic benthic ∂18O (climate) and carbon cycle records (∂13C, and 20-0 Ma pCO2). Warmer climates are strongly correlated with lower diatom diversity (raw: rho = .92, p2 were only moderately higher than today. Diversity is strongly correlated to both ∂13C and pCO2 over the last 15 my (for both: r>.9, detrended r>.6, all p<.001), but only weakly over the earlier Cenozoic, suggesting increasingly strong linkage of diatom and climate evolution in the Neogene. Our results suggest that many living marine planktonic diatom species may be at risk of extinction in future warm oceans, with an unknown but potentially substantial negative impact on the ocean biologic pump and oceanic carbon sequestration. We cannot however extrapolate our my-scale correlations with generic climate proxies to anthropogenic time-scales of warming without additional species-specific information on proximate ecologic controls.

Observation of visible emission from the molecular helium ion in the afterglow of a dense helium Z-pinch plasma

International Nuclear Information System (INIS)

Tucker, J.E.; Brake, M.L.; Gilgenbach, R.M.

1986-01-01

The authors present the results of axial and radial time resolved visible emission spectroscopy from the afterglow of a dense helium Z-pinch. These results show that the visible emissions in the pinch afterglow are dominated by line emissions from molecular helium and He II. Axial spectroscopy measurements show the occurrence of several absorption bands which cannot be identified as molecular or atomic helium nor impurities from the discharge chamber materials. The authors believe that these absorption bands are attributable to the molecular helium ion which is present in the discharge. The molecular ion has been observed by others in low pressure and temperature helium discharges directly by means of mass spectrometry and indirectly by the presence of helium atoms in the 2/sup 3/S state, (the He 2/sup 3/S state is believed to result from molecular helium ion recombination). However, the molecular helium ion has not previously been observed spectroscopically

Diatom flora in subterranean ecosystems: a review

Directory of Open Access Journals (Sweden)

Elisa Falasco

2014-09-01

Full Text Available In scarcity of light and primary producers, subterranean ecosystems are generally extremely oligotrophic habitats, receiving poor supplies of degradable organic matter from the surface. Human direct impacts on cave ecosystems mainly derive from intensive tourism and recreational caving, causing important alterations to the whole subterranean environment. In particular, artificial lighting systems in show caves support the growth of autotrophic organisms (the so-called lampenflora, mainly composed of cyanobacteria, diatoms, chlorophytes, mosses and ferns producing exocellular polymeric substances (EPSs made of polysaccharides, proteins, lipids and nucleic acids. This anionic EPSs matrix mediates to the intercellular communications and participates to the chemical exchanges with the substratum, inducing the adsorption of cations and dissolved organic molecules from the cave formations (speleothems. Coupled with the metabolic activities of heterotrophic microorganisms colonising such layer (biofilm, this phenomenon may lead to the corrosion of the mineral surfaces. In this review, we investigate the formation of biofilms, especially of diatom-dominated ones, as a consequence of artificial lighting and its impacts on speleothems. Whenever light reaches the subterranean habitat (both artificially and naturally a relative high number of species of diatoms may indeed colonise it. Cave entrances, artificially illuminated walls and speleothems inside the cave are generally the preferred substrates. This review focuses on the diatom flora colonising subterranean habitats, summarizing the information contained in all the scientific papers published from 1900 up to date. In this review we provide a complete checklist of the diatom taxa recorded in subterranean habitats, including a total of 363 taxa, belonging to 82 genera. The most frequent and abundant species recorded in caves and other low light subterranean habitats are generally aerophilic and

Molecular desorption of stainless steel vacuum chambers irradiated with 4.2 MeV/u lead ions

CERN Document Server

Mahner, E; Laurent, Jean Michel; Madsen, N

2003-01-01

In preparation for the heavy ion program of the Large Hadron Collider (LHC) at CERN, accumulation and cooling tests with lead ion beams have been performed in the Low Energy Antiproton Ring (LEAR). These tests have revealed that due to the unexpected large outgassing of the vacuum system, the dynamic pressure of the ring could not be maintained low enough to reach the required beam intensities. To determine the actions necessary to lower the dynamic pressure rise, an experimental program has been initiated for measuring the molecular desorption yields of stainless steel vacuum chambers by the impact of 4.2 MeV/u lead ions with the charge states +27 and +53. The test chambers were exposed either at grazing or at perpendicular incidence. Different surface treatments (glow-discharges, non-evaporable getter coating) are reported in terms of the molecular desorption yields for H2, CH4, CO, Ar and CO2. Unexpected large values of molecular yields per incident ion up to 2 104 molecules/ion have been observed. The red...

Relationships between diatoms and tidal environments in Oregon and Washington, USA

Science.gov (United States)

Sawai, Yuki; Horton, Benjamin P.; Kemp, Andrew C.; Hawkes, Andrea D.; Nagumo, Tamostsu; Nelson, Alan R.

2016-01-01

A new regional dataset comprising 425 intertidal diatom taxa from 175 samples from 11 ecologically diverse Oregon and Washington estuaries illustrates the importance of compiling a large modern dataset from a range of sites. Cluster analyses and detrended correspondence analysis of the diatom assemblages identify distinct vertical zones within supratidal, intertidal and subtidal environments at six of the 11 study sites, but the abundance of some of the most common species varies widely among and within sites. Canonical correspondence analysis of the regional dataset shows relationships between diatom species and tidal exposure, salinity and substratum (grain size and organic content). Correspondence analyses of local datasets show higher values of explained variation than the analysis of the combined regional dataset. Our results emphasize that studies of the autecology of diatom species require many samples from a range of modern environments to adequately characterize species–environment relationships.

The UV filtering potential of drop-casted layers of frustules of three diatom species

DEFF Research Database (Denmark)

Su, Yanyan; Lenau, Torben Anker; Gundersen, Emil

2018-01-01

Diatoms are in focus as biological materials for a range of photonic applications. Many of theseapplications would require embedding a multitude of diatoms in a matrix (e.g. paint, crème or lacquer); however, most studies on the photonic and spectral properties of diatoms frustules (silica walls)...

Diatoms as a fingerprint of sub-catchment contributions to meso-scale catchment runoff

Science.gov (United States)

Klaus, Julian; Wetzel, Carlos E.; Martinez-Carreras, Nuria; Ector, Luc; Pfister, Laurent

2014-05-01

In recent years, calls were made for new eco-hydrological approaches to improve understanding of hydrological processes. Recently diatoms, one of the most common and diverse algal groups that can be easily transported by flowing water due to their small size (~10-200 µm), were used to detect the onset and cessation of surface runoff to small headwater streams and constrain isotopic and hydro-chemical hydrograph separation methods. While the method showed its potential in the hillslope-riparian zone-stream continuum of headwater catchments, the behavior of diatoms and their use for hydrological process research in meso-scale catchments remains uncertain. Diatoms can be a valuable support for isotope and hydro-chemical tracer methods when these become ambiguous with increasing scale. Distribution and abundance of diatom species is controlled by various environmental factors (pH, soil type, moisture conditions, exposition to sunlight, etc.). We therefore hypothesize that species abundance and composition can be used as a proxy for source areas. This presentation evaluates the potential for diatoms to trace source-areas in the nested meso-scale Attert River basin (250 km2, Luxembourg, Europe). We sampled diatom populations in streamwater during one flood event in Fall 2011 in 6 sub-catchments and the basin outlet - 17 to 28 samples/catchment for the different sampling locations. Diatoms were classified and counted in every individual sample. In total more than 400 diatom species were detected. Ordination analysis revealed a clear distinction between communities sampled in different sub-catchments. The species composition at the catchment outlet reflects a mixing of the diatom composition originating from different sub-catchments. This data suggests that diatoms indeed can reflect the geographic origin of stream water at the catchment outlet. The centroids of the ordination analysis might be linked to the physiographic characteristics (geology and land use) of the

Photodissociation spectroscopy of the dysprosium monochloride molecular ion

Energy Technology Data Exchange (ETDEWEB)

Dunning, Alexander, E-mail: alexander.dunning@gmail.com; Schowalter, Steven J.; Puri, Prateek; Hudson, Eric R. [Department of Physics and Astronomy, University of California, Los Angeles, California 90095 (United States); Petrov, Alexander; Kotochigova, Svetlana [Department of Physics, Temple University, Philadelphia, Pennsylvania 19122 (United States)

2015-09-28

We have performed a combined experimental and theoretical study of the photodissociation cross section of the molecular ion DyCl{sup +}. The photodissociation cross section for the photon energy range 35 500 cm{sup −1} to 47 500 cm{sup −1} is measured using an integrated ion trap and time-of-flight mass spectrometer; we observe a broad, asymmetric profile that is peaked near 43 000 cm{sup −1}. The theoretical cross section is determined from electronic potentials and transition dipole moments calculated using the relativistic configuration-interaction valence-bond and coupled-cluster methods. The electronic structure of DyCl{sup +} is extremely complex due to the presence of multiple open electronic shells, including the 4f{sup 10} configuration. The molecule has nine attractive potentials with ionically bonded electrons and 99 repulsive potentials dissociating to a ground state Dy{sup +} ion and Cl atom. We explain the lack of symmetry in the cross section as due to multiple contributions from one-electron-dominated transitions between the vibrational ground state and several resolved repulsive excited states.

Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula

KAUST Repository

Pearson, Gareth A

2015-04-14

Functional genomics of diatom-dominated communities fromthe Antarctic Peninsula was studied using comparative metatranscriptomics. Samples obtained from diatom-rich communities in the Bransfield Strait, the western Weddell Sea and sea ice in the Bellingshausen Sea/Wilkins Ice Shelf yielded more than 500K pyrosequencing reads that were combined to produce a global metatranscriptome assembly. Multi-gene phylogenies recovered three distinct communities, and diatom-assigned contigs further indicated little read-sharing between communities, validating an assembly-based annotation and analysis approach. Although functional analysis recovered a core of abundant shared annotations that were expressed across the three diatom communities, over 40% of annotations (but accounting for <10% of sequences) were community-specific. The two pelagic communities differed in their expression of N-metabolism and acquisition genes, which was almost absent in post-bloom conditions in the Weddell Sea community, while enrichment of transporters for ammonia and urea in Bransfield Strait diatoms suggests a physiological stance towards acquisition of reduced N-sources. The depletion of carbohydrate and energy metabolism pathways in sea ice relative to pelagic communities, together with increased light energy dissipation (via LHCSR proteins), photorespiration, and NO3 - uptake and utilization all pointed to irradiance stress and/or inorganic carbon limitation within sea ice. Ice-binding proteins and cold-shock transcription factors were also enriched in sea ice diatoms. Surprisingly, the abundance of gene transcripts for the translational machinery tracked decreasing environmental temperature across only a 4 °C range, possibly reflecting constraints on translational efficiency and protein production in cold environments. © 2015 International Society for Microbial Ecology All rights reserved.

Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula

KAUST Repository

Pearson, Gareth A; Lago-Leston, Asuncion; Cá novas, Fernando; Cox, Cymon J; Verret, Frederic; Lasternas, Sebastian; Duarte, Carlos M.; Agusti, Susana; Serrã o, Ester A

2015-01-01

Functional genomics of diatom-dominated communities fromthe Antarctic Peninsula was studied using comparative metatranscriptomics. Samples obtained from diatom-rich communities in the Bransfield Strait, the western Weddell Sea and sea ice in the Bellingshausen Sea/Wilkins Ice Shelf yielded more than 500K pyrosequencing reads that were combined to produce a global metatranscriptome assembly. Multi-gene phylogenies recovered three distinct communities, and diatom-assigned contigs further indicated little read-sharing between communities, validating an assembly-based annotation and analysis approach. Although functional analysis recovered a core of abundant shared annotations that were expressed across the three diatom communities, over 40% of annotations (but accounting for <10% of sequences) were community-specific. The two pelagic communities differed in their expression of N-metabolism and acquisition genes, which was almost absent in post-bloom conditions in the Weddell Sea community, while enrichment of transporters for ammonia and urea in Bransfield Strait diatoms suggests a physiological stance towards acquisition of reduced N-sources. The depletion of carbohydrate and energy metabolism pathways in sea ice relative to pelagic communities, together with increased light energy dissipation (via LHCSR proteins), photorespiration, and NO3 - uptake and utilization all pointed to irradiance stress and/or inorganic carbon limitation within sea ice. Ice-binding proteins and cold-shock transcription factors were also enriched in sea ice diatoms. Surprisingly, the abundance of gene transcripts for the translational machinery tracked decreasing environmental temperature across only a 4 °C range, possibly reflecting constraints on translational efficiency and protein production in cold environments. © 2015 International Society for Microbial Ecology All rights reserved.

Diatom distribution in the surficial sediments of Lake Fuxian, Yunnan ...

African Journals Online (AJOL)

ajl yemi

2011-11-30

Nov 30, 2011 ... The diatom abundances per gram dry weight sediment vary between 18.4 × 106 and 66.9 × 106 valves (Figure 2). Abundances per gram dry weight of the eight most abundant diatom taxa are shown in Figure 3. The DCA diagram shows centroids of ecoregions in the ordination space of the first axes.

Interference patterns and extinction ratio of the diatom Coscinodiscus granii

DEFF Research Database (Denmark)

Maibohm, Christian; Friis, Søren Michael Mørk; Ellegaard, M.

2015-01-01

We report experimental and theoretical verification of the nature and position of multiple interference points of visible light transmitted through the valve of the centric diatom species Coscinodiscus granii. Furthermore, by coupling the transmitted light into an optical fiber and moving...... the diatom valve between constructive and destructive interference points, an extinction ratio of 20 dB is shown...

Spatial and energy distributions of the fragments resulting from the dissociation of swift molecular ions in solids

International Nuclear Information System (INIS)

Heredia-Avalos, Santiago; Garcia-Molina, Rafael; Abril, Isabel

2002-01-01

We have simulated the spatial evolution and energy loss of the fragments that result when swift molecular ions dissociate inside solid targets. In our calculations we have considered that these fragments undergo the following interactions: Coulomb repulsion (among like charged particles), stopping and wake forces (due to electronic excitations induced in the target), and nuclear scattering (with the target nuclei). We study the case of silicon targets irradiated with boron molecular or atomic ions; our results show that the main differences in the energy and spatial distributions of molecular fragments or atomic ions appear at shallow regions, and these tend to disappear at deeper depths

Use of Moeller-Plesset perturbation theory in molecular calculations: Spectroscopic constants of first row diatomic molecules

International Nuclear Information System (INIS)

Dunning, T.H. Jr.; Peterson, K.A.

1998-01-01

The convergence of Moeller - Plesset perturbation expansions (MP2 - MP4/MP5) for the spectroscopic constants of a selected set of diatomic molecules (BH, CH, HF, N 2 , CO, and F 2 ) has been investigated. It was found that the second-order perturbation contributions to the spectroscopic constants are strongly dependent on basis set, more so for HF and CO than for BH. The MP5 contributions for HF were essentially zero for the cc-pVDZ basis set, but increased significantly with basis set illustrating the difficulty of using small basis sets as benchmarks for correlated calculations. The convergence behavior of the exact Moeller - Plesset perturbation expansions were investigated using estimates of the complete basis set limits obtained using large correlation consistent basis sets. For BH and CH, the perturbation expansions of the spectroscopic constants converge monotonically toward the experimental values, while for HF, N 2 , CO, and F 2 , the expansions oscillate about the experimental values. The perturbation expansions are, in general, only slowly converging and, for HF, N 2 , CO, and F 2 , appear to be far from convergence at MP4. In fact, for HF, N 2 , and CO, the errors in the calculated spectroscopic constants for the MP4 method are larger than those for the MP2 method (the only exception is D e ). The current study, combined with other recent studies, raises serious doubts about the use of Moeller - Plesset perturbation theory to describe electron correlation effects in atomic and molecular calculations. copyright 1998 American Institute of Physics

Fouling diatom community with reference to substratum variability in tropical marine environment

Digital Repository Service at National Institute of Oceanography (India)

Mitbavkar, S.; Desai, D.V.; Khandeparker, L.; Anil, A.C.; Wagh, A.B.

form encountered. The paper deals with the qualitative and quantitative aspects of diatom colonization, their community structure, and correlation between the prevailing diatom population in the environment and that in the fouling community...

Seasonal and daily fluctuation of diatoms during spring tide periods in Kerkennah Islands

Directory of Open Access Journals (Sweden)

Mounir Ben brahim

2015-06-01

Full Text Available Objective: To study seasonal and the daily distribution of diatoms in the three tidal periods (flood, slack and ebb period during the spring tide. Methods: Water samples were taken and environmental variables were measured three times in each tidal period during 10 days of spring tide. Sampling was done in 2007 in Cercina station located in the western coast of Kerkennah (34°41'27'' N; 11°07'45'' E (Southern Tunisia. Results: Nutrients showed significant variation between seasons, increasing in spring and decreasing noticeably in autumn and winter. About 36 diatom species were found. Results revealed a remarkable abundance increase in spring and summer. Irregular differences in diatom abundances were revealed over the tidal periods, with the highest rates being detected during the flood and the ebb period, while the abundance rate was lowest during the slack period. This could presumably be attributed to the increase of nutrient supply of suspended particulate matter during water motion. The results revealed a correlation between diatom abundance and temperature, NO2 - , NO3 - , Si(OH4 and PO4 3 . Temperature seemed to be the most important factors which may influence the distribution and diatom abundance. Conclusions: Tide has various effects on the nutrients status and diatoms community (in terms of species composition, succession and abundance between different tidal periods. Fluctuation of diatoms was correlated with changes in the circulation of water bodies and changes in nutrient regime.

The exotic molecular ion H43+ in a strong magnetic field

International Nuclear Information System (INIS)

Olivares P, H.

2006-01-01

Using the variational method, a detailed study of the lowest m = 0, -1 electronic states of the exotic molecular ion H3+ 4 in a strong magnetic field, in the linear symmetric configuration parallel to the direction of the magnetic field is carried out. A extended study of the 1σg ground state (J.C. Lopez and A.Turbiner, Phys. Rev A 62, 022510, 2000) was performed obtaining that the potential energy curve displays a sufficiently deep minimum for finite internuclear distances, indicating the possible existence of the molecular ion H 4 3+ , for magnetic fields of strength B > ∼ 3 x 10 13 G. It is demonstrated that the excited state 1π u , can exist for a magnetic field B = 4.414 x 10 13 G corresponding to the limit of applicability of the non-relativistic theory. (Author)

Trapped ultracold molecular ions: candidates for an optical molecular clock for a fundamental physics mission in space

Science.gov (United States)

Roth, B.; Koelemeij, J.; Daerr, H.; Ernsting, I.; Jorgensen, S.; Okhapkin, M.; Wicht, A.; Nevsky, A.; Schiller, S.

2017-11-01

Narrow ro-vibrational transitions in ultracold molecules are excellent candidates for frequency references in the near-IR to visible spectral domain and interesting systems for fundamental tests of physics, in particular for a satellite test of the gravitational redshift of clocks. We have performed laser spectroscopy of several ro-vibrational overtone transitions υ = 0 → υ = 4 in HD+ ions at around 1.4 μm. 1+1 REMPD was used as a detection method, followed by measurement of the number of remaining molecules. The molecular ions were stored in a linear radiofrequency trap and cooled to millikelvin temperatures, by sympathetic cooling using laser-cooled Be+ ions simultaneously stored in the same trap.

THE RESPONSE OF THE PERIPHYTIC DIATOM COMMUNITY TO ACID MINE DRAINAGE POLLUTION

Directory of Open Access Journals (Sweden)

Andreea Ciorba

2004-01-01

Full Text Available This paper proposes to relate the principal characteristics of diatom community (species richness, biodiversity, community biomass, diatom indices to the stress induced by acidification and high levels of metal. The study was done in a mine drainage affected area in Galicia (NW Spain by comparing periphytic diatom communities from polluted streams to ones in supposedly clean waters. The change in the dominant species was the clearest response to AMD pollution while species richness and diversity were sensitive only to high levels of pollution.

Measurement of the density profile of pure and seeded molecular beams by femtosecond ion imaging

Energy Technology Data Exchange (ETDEWEB)

Meng, Congsen [LaserLaB Amsterdam, VU University Amsterdam, de Boelelaan 1083, 1081 HV Amsterdam (Netherlands); Department of Physics, National University of Defense Technology, Changsha 410073 (China); Janssen, Maurice H. M. [LaserLaB Amsterdam, VU University Amsterdam, de Boelelaan 1083, 1081 HV Amsterdam (Netherlands)

2015-02-15

Here, we report on femtosecond ion imaging experiments to measure the density profile of a pulsed supersonic molecular beam. Ion images are measured for both a molecular beam and bulk gas under identical experimental conditions via femtosecond multiphoton ionization of Xe atoms. We report the density profile of the molecular beam, and the measured absolute density is compared with theoretical calculations of the centre line beam density. Subsequently, we discuss reasons accounting for the differences between measurements and calculations and propose that strong skimmer interference is the most probable cause for the differences. Furthermore, we report on experiments measuring the centre line density of seeded supersonic beams. The femtosecond ion images show that seeding the heavy Xe atom at low relative seed fractions (1%-10%) in a light carrier gas like Ne results in strong relative enhancements of up to two orders of magnitude.

Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

Science.gov (United States)

Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

2018-06-01

We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

Growth inhibition of periphytic diatoms by methanol extracts of sponges and holothurians

Digital Repository Service at National Institute of Oceanography (India)

Mokashe, S.S.; Garg, A; Anil, A; Wagh, A

Crude methanol extracts of a holothurian Holothuria leucospilota, and two sponges Craniella sp. and Ircinia ramosa were tested for their inhibitory effects on the growth of two marine diatoms, Navicula subinflata and N. crucicula, by diatom plating...

Statistical analysis of dimer formation in supersaturated metal vapor based on molecular dynamics simulation

Science.gov (United States)

Korenchenko, Anna E.; Vorontsov, Alexander G.; Gelchinski, Boris R.; Sannikov, Grigorii P.

2018-04-01

We discuss the problem of dimer formation during the homogeneous nucleation of atomic metal vapor in an inert gas environment. We simulated nucleation with molecular dynamics and carried out the statistical analysis of double- and triple-atomic collisions as the two ways of long-lived diatomic complex formation. Close pair of atoms with lifetime greater than the mean time interval between atom-atom collisions is called a long-lived diatomic complex. We found that double- and triple-atomic collisions gave approximately the same probabilities of long-lived diatomic complex formation, but internal energy of the resulted state was essentially lower in the second case. Some diatomic complexes formed in three-particle collisions are stable enough to be a critical nucleus.

Effect of ageing on survival of benthic diatom propagules

Digital Repository Service at National Institute of Oceanography (India)

Anil, A.C.; Mitbavkar, S.; De; Hegde, S.; De; Meher, S.S.; Banerjee, D.

unfavorable for vegetative growth, many diatoms form resting stages to survive cell degradation or death (Anderson, 1975; Malone, 1980; Hargraves and French, 1983; Fryxell, 1990). Various external factors like availability of nutrients (N, P, Fe, Si.... 128, 497-508. 15 Lewis, J., Harris, A.S.D., Jones, K.J., Edmonds, R.L., 1999. Long-term survival of marine planktonic diatoms and dinoflagellates in stored sediment samples. J. Plank. Res. 21, 343- 354. Malone, T.C., 1980. Algal size. In...

Nature engineered diatom biosilica as drug delivery systems.

Science.gov (United States)

Uthappa, U T; Brahmkhatri, Varsha; Sriram, G; Jung, Ho-Young; Yu, Jingxian; Kurkuri, Nikita; Aminabhavi, Tejraj M; Altalhi, Tariq; Neelgund, Gururaj M; Kurkuri, Mahaveer D

2018-05-14

Diatoms, unicellular photosynthetic algae covered with siliceous cell wall, are also called frustule. These are the most potential naturally available materials for the development of cost-effective drug delivery systems because of their excellent biocompatibility, high surface area, low cost and ease of surface modification. Mesoporous silica materials such as MCM-41 and SBA-15 have been extensively used in drug delivery area. Their synthesis is challenging, time consuming, requires toxic chemicals and are energy intensive, making the entire process expensive and non-viable. Therefore, it is necessary to explore alternative materials. Surprisingly, nature has provided some exciting materials called diatoms; biosilica is one such a material that can be potentially used as a drug delivery vehicle. The present review focuses on different types of diatom species used in drug delivery with respect to their structural properties, morphology, purification process and surface functionalization. In this review, recent advances along with their limitations as well as the future scope to develop them as potential drug delivery vehicles are discussed. Copyright © 2018. Published by Elsevier B.V.

Static vs dynamic settlement and adhesion of diatoms to ship hull coatings.

Science.gov (United States)

Zargiel, Kelli A; Swain, Geoffrey W

2014-01-01

Many experiments utilize static immersion tests to evaluate the performance of ship hull coatings. These provide valuable data; however, they do not accurately represent the conditions both the hull and fouling organisms encounter while a ship is underway. This study investigated the effect of static and dynamic immersion on the adhesion and settlement of diatoms to one antifouling coating (BRA 640), four fouling-release coatings (Intersleek(®) 700, Intersleek(®) 900, Hempasil X3, and Dow Corning 3140) and one standard surface (Intergard(®) 240 Epoxy). Differences in community composition were observed between the static and dynamic treatments. Achnanthes longipes was present on all coatings under static immersion, but was not present under dynamic immersion. This was also found for diatoms in the genera Bacillaria and Gyrosigma. Melosira moniformis was the only diatom present under dynamic conditions, but not static conditions. Several common fouling diatom genera were present on panels regardless of treatment: Amphora, Cocconeis, Entomoneis Cylindrotheca, Licmophora, Navicula, Nitzschia, Plagiotropis, and Synedra. Biofilm adhesion, diatom abundance and diatom diversity were found to be significantly different between static and dynamic treatments; however, the difference was dependent on coating and sampling date. Several coatings (Epoxy, DC 3140 and IS 700) had significantly higher biofilm adhesion on dynamically treated panels on at least one of the four sampling dates, while all coatings had significantly higher diatom abundance on at least one sampling date. Diversity was significantly greater on static panels than dynamic panels for Epoxy, IS 700 and HX3 at least once during the sampling period. The results demonstrate how hydrodynamic stress will significantly influence the microfouling community. Dynamic immersion testing is required to fully understand how antifouling surfaces will respond to biofilm formation when subjected to the stresses experienced

Circular random motion in diatom gliding under isotropic conditions

International Nuclear Information System (INIS)

Gutiérrez-Medina, Braulio; Maldonado, Ana Iris Peña; Guerra, Andrés Jiménez; Rubio, Yadiralia Covarrubias; Meza, Jessica Viridiana García

2014-01-01

How cells migrate has been investigated primarily for the case of trajectories composed by joined straight segments. In contrast, little is known when cellular motion follows intrinsically curved paths. Here, we use time-lapse optical microscopy and automated trajectory tracking to investigate how individual cells of the diatom Nitzschia communis glide across surfaces under isotropic environmental conditions. We find a distinct kind of random motion, where trajectories are formed by circular arcs traveled at constant speed, alternated with random stoppages, direction reversals and changes in the orientation of the arcs. Analysis of experimental and computer-simulated trajectories show that the circular random motion of diatom gliding is not optimized for long-distance travel but rather for recurrent coverage of limited surface area. These results suggest that one main biological role for this type of diatom motility is to efficiently build the foundation of algal biofilms. (paper)

Energetic atomic and molecular ions of ionospheric origin observed in distant magnetotail flow-reversal events

Science.gov (United States)

Christon, S. P.; Gloeckler, G.; Williams, D. J.; Mukai, T.; Mcentire, R. W.; Jacquey, C.; Angelopoulos, V.; Lui, A. T. Y.; Kokubun, S.; Fairfield, D. H.

1994-01-01

Energetic atomic (O(+1) and N(+1)) and molecular (O2(+1), NO(+1), and N2(+1)) ions of ionospheric origin were observed in Earth's magnetotail at X approximately -146 R(sub E) during two plasma sheet sunward/tailward flow-reversal events measured by instruments on the GEOTAIL spacecraft. These events were associated with concurrent ground-measured geomagnetic disturbance intensification at auroral-and mid-latitudes (Kp = 7(-)). Energetic ions in the sunward-component and tailward flows were from both the solar wind and ionosphere. Plasma and energetic ions participated in the flows. During tailward flow, ionospheric origin ion abundance ratios at approximately 200-900 km/s in the rest frame were N(+1)/O(+1) = approximately 25-30% and ((O2(+1), NO(+1), and N2(+1))/O(+1) = approximately 1-2%. We argue that tailward flow most likely initiated approximately 80-100 R(sub E) tailward of Earth and molecular ions were in the plasma sheet prior to geomagnetic intensification onset.

Aldehyde suppression of copepod recruitment in blooms of a ubiquitous planktonic diatom

Science.gov (United States)

Ianora, Adrianna; Miralto, Antonio; Poulet, Serge A.; Carotenuto, Ylenia; Buttino, Isabella; Romano, Giovanna; Casotti, Raffaella; Pohnert, Georg; Wichard, Thomas; Colucci-D'Amato, Luca; Terrazzano, Giuseppe; Smetacek, Victor

2004-05-01

The growth cycle in nutrient-rich, aquatic environments starts with a diatom bloom that ends in mass sinking of ungrazed cells and phytodetritus. The low grazing pressure on these blooms has been attributed to the inability of overwintering copepod populations to track them temporally. We tested an alternative explanation: that dominant diatom species impair the reproductive success of their grazers. We compared larval development of a common overwintering copepod fed on a ubiquitous, early-blooming diatom species with its development when fed on a typical post-bloom dinoflagellate. Development was arrested in all larvae in which both mothers and their larvae were fed the diatom diet. Mortality remained high even if larvae were switched to the dinoflagellate diet. Aldehydes, cleaved from a fatty acid precursor by enzymes activated within seconds after crushing of the cell, elicit the teratogenic effect. This insidious mechanism, which does not deter the herbivore from feeding but impairs its recruitment, will restrain the cohort size of the next generation of early-rising overwinterers. Such a transgenerational plant-herbivore interaction could explain the recurringly inefficient use of a predictable, potentially valuable food resource-the spring diatom bloom-by marine zooplankton.

Atmospheric-pressure solution-cathode glow discharge: A versatile ion source for atomic and molecular mass spectrometry

Energy Technology Data Exchange (ETDEWEB)

Schwartz, Andrew J. [Department of Chemistry, Indiana University, Bloomington, IN, 47405 (United States); Williams, Kelsey L. [Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242 (United States); Hieftje, Gary M. [Department of Chemistry, Indiana University, Bloomington, IN, 47405 (United States); Shelley, Jacob T., E-mail: shellj@rpi.edu [Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242 (United States); Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180 (United States)

2017-01-15

An atmospheric-pressure solution-cathode glow discharge (SCGD) has been evaluated as an ion source for atomic, molecular, and ambient desorption/ionization mass spectrometry. The SCGD consists of a direct-current plasma, supported in the ambient air in the absence of gas flows, and sustained upon the surface of a flowing liquid cathode. Analytes introduced in the flowing liquid, as an ambient gas, or as a solid held near the plasma are vaporized and ionized by interactions within or near the discharge. Introduction of acidic solutions containing metal salts produced bare elemental ions as well as H{sub 2}O, OH{sup −} and NO{sub 3}{sup −} adducts. Detection limits for these elemental species ranged from 0.1 to 4 ppb, working curves spanned more than 4 orders of linear dynamic range, and precision varied between 5 and 16% relative standard deviation. Small organic molecules were also efficiently ionized from solution, and both the intact molecular ion and fragments were observed in the resulting SCGD mass spectra. Fragmentation of molecular species was found to be tunable; high discharge currents led to harder ionization, while low discharge currents produced stronger molecular-ion signals. Ambient gases and solids, desorbed by the plasma from a glass probe, were also readily ionized by the SCGD. Indeed, strong analyte signals were obtained from solid samples placed at least 2 cm from the plasma. These findings indicate that the SCGD might be useful also for ambient desorption/ionization mass spectrometry. Combined with earlier results that showed the SCGD is useful for ionization of labile biomolecules, the results here indicate that the SCGD is a highly versatile ion source capable of providing both elemental and molecular mass-spectral information. - Highlights: • Solution-cathode glow discharge used as an ionization source for mass spectrometry. • SCGD-MS can provide atomic as well as intact molecular mass spectra. • Atomic limits of detection range

Do diatoms percolate through soil and can they be used for tracing the origin of runoff?

Science.gov (United States)

De Graaf, Lenka; Cammeraat, Erik; Pfister, Laurent; Wetzel, Carlos; Klaus, Julian; Hissler, Christophe

2015-04-01

Tracers are widely used to study the movement of water in a catchment. Because of depletion of scientific possibilities with most common tracer types, we proposed the use of diatoms as a natural tracer. Paradoxical results on the contribution of surface runoff to the storm hydrograph were obtained in pioneer research on this idea. Diatom transport via the subsurface flow to the stream would explain this paradox. Prerequisite for this is vertical transport of diatoms through soils, which is the topic of this study. Emphasis is on percolation behavior (speed of percolation, speed of percolation over time, and species distribution) of Pseudostaurosira sp. and Melosira sp. (Bacillariophyceae) through undisturbed soil columns of contrasting substrates. Co-objective is to study the flowpaths of water through the soil columns. Natural undisturbed soil columns were sampled in the Attert basin (Luxembourg) on schist, marl and sandstone substrates. Rain simulation experiments were performed to study vertical diatom transport. Rhodamine dye experiments were carried out to gain insight in the active flowpaths of water, and breakthrough experiments were performed to study the responses of the soil columns to applied water. Diatoms were transported through the soil columns of the three substrates. A vast majority of diatom percolation took place within the first 15 minutes, percolation hereafter was marginal but nevertheless present. Peaks in diatom percolation corresponded with a high flux caused by the addition of the diatom culture, but seepage of diatoms along the sides is unlikely according to the species distribution and the rhodamine dye experiment. Pseudostaurosira sp. percolated significantly better than Melosira sp. Significantly more diatoms percolated through the marl columns compared to the schist columns and variance within the sandstone group was very high. Absolute differences between substrates however, were marginal. Most preferential flowpaths were observed in

Dissociation of fast HeH+ ions in foils and gases

International Nuclear Information System (INIS)

Gemmell, D.S.; Cooney, P.J.; Pietsch, W.J.; Ratkowski, A.J.; Vager, Z.

1978-01-01

To gain understanding of phenomena observed when very simple light diatomic ions are incident at high velocities upon thin foils and gaseous targets, an extensive set of measurements on the dissociation products arising from beams of HeH + was made. Experimental and calculated joint distributions in energy and angle for protons emerging (near the beam direction) from an 85-A carbon foil bombarded by 2.0-MeV HeH + ions are presented

Si and C interactions in the world ocean: Importance of ecological processes and implications for the role of diatoms in the biological pump

Science.gov (United States)

Ragueneau, Olivier; Schultes, Sabine; Bidle, Kay; Claquin, Pascal; Moriceau, BrivaëLa

2006-12-01

Diatoms play a major role in carbon export from surface waters, but their role in the transport of carbon to the deep sea has been questioned by global analyses of sediment trap fluxes which suggest that organic carbon fluxes and transfer efficiencies through the mesopelagic are tightly correlated with CaCO3 (Klaas and Archer, 2002; François et al., 2002). Here we explore the role of diatoms in the biological pump through a study of Si and C interactions from the molecular to the global scale. Recent findings on molecular interactions between Si and C are reviewed. The roles of bacteria, grazers and aggregation are explored and combined, to account for the extent of Si and C decoupling between surface waters and 1000 m, observed to be very homogeneous in different biogeochemical provinces of the ocean. It is suggested that the mesopelagic food web plays a crucial role in this homogeneity: Sites of high export are also sites where diatom C is being either remineralized or channeled toward the long-lived carbon pool most efficiently in the mesopelagic zone. The amount of carbon participating in the biological pump but not collected in sediment traps remains to be explored. It is also demonstrated that statistical analyses performed at global scales hide spatial variability in carrying coefficients, indicating a clear need to understand the mechanisms that control spatial and temporal variations in the relative importance of ballast minerals and other export mechanisms such as particle dynamics.

Molecular models of alginic acid: Interactions with calcium ions and calcite surfaces

Science.gov (United States)

Perry, Thomas D.; Cygan, Randall T.; Mitchell, Ralph

2006-07-01

Cation binding by polysaccharides is observed in many environments and is important for predictive environmental modeling, and numerous industrial and food technology applications. The complexities of these cation-organic interactions are well suited for predictive molecular modeling and the analysis of conformation and configuration of polysaccharides and their influence on cation binding. In this study, alginic acid was chosen as a model polymer system and representative disaccharide and polysaccharide subunits were developed. Molecular dynamics simulation of the torsion angles of the ether linkage between various monomeric subunits identified local and global energy minima for selected disaccharides. The simulations indicate stable disaccharide configurations and a common global energy minimum for all disaccharide models at Φ = 274 ± 7°, Ψ = 227 ± 5°, where Φ and Ψ are the torsion angles about the ether linkage. The ability of disaccharide subunits to bind calcium ions and to associate with the (101¯4) surface of calcite was also investigated. Molecular models of disaccharide interactions with calcite provide binding energy differences for conformations that are related to the proximity and residence densities of the electron-donating moieties with calcium ions on the calcite surface, which are controlled, in part, by the torsion of the ether linkage between monosaccharide units. Dynamically optimized configurations for polymer alginate models with calcium ions were also derived.

Molecular Dynamics Simulation of the Antiamoebin Ion Channel: Linking Structure and Conductance

Science.gov (United States)

Wilson, Michael A.; Wei, Chenyu; Bjelkmar, Paer; Wallace, B. A.; Pohorille, Andrew

2011-01-01

Molecular dynamics simulations were carried out in order to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistant with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive.The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be non-conducting. The conductance of the hexamer was estimated to be 115+/-34 pS and 74+/-20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K(+) and Cl(-) with their first solvation shells intact. The free energy barrier encountered by K(+) is only 2.2 kcal/mol whereas Cl(-) encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics. keywords: ion channels, peptaibols, channel conductance, molecular dynamics

Molecular structure studies by 3D imaging of fast ion beams

International Nuclear Information System (INIS)

Kanter, E.P.; Vager, Z.; Both, G.; Cooney, P.J.; Faibis, A.; Koenig, W.; Zabransky, B.J.; Zajfman, D.

1986-01-01

The use of the Coulomb-explosion technique combined with a radically new multi-particle detector, extremely thin film targets, and low-excitation ion source has enabled, for the first time, direct measurements of the complete stereochemistry of complex polyatomic molecular ions. We outline the methods used and present results for protonated acetylene (C 2 H 3 + ) and the methane cation (CH 4 + ) as examples. We demonstrate the techniques by which these methods can be generalized to determine directly vibrational motions in polyatomic molecules. 24 refs., 4 figs

Calculated Cross Sections for the Electron Impact Ionization of Molecular Ions

Science.gov (United States)

Deutsch, H.; Becker, K.; Defrance, P.; Onthong, U.; Parajuli, R.; Probst, M.; Matt-Leubner, S.; Maerk, T.

2002-10-01

We report the results of the application of the semi- classical Deutsch-Märk (DM) formalism to the calculation of the absolute electron-impact ionization cross section of the molecular ions H2+, N2+, O2+, CD+, CO+, CO2+, H3O+, and CH4+ for which experimental data have been reported . Where available, we also compare our calculated cross sections with calculated cross sections using the BEB method of Kim and co-workers. The level of agreement between the experimentally determined and calculated cross section is satisfactory in some cases. In all cases, the calculated cross sections exceed the measured cross sections which is not surprising in view of the experimental complications in measuring ionization cross sections of molecular ions due to the presence of competing channels such as ionization dissociative ionization, and dissociative excitation. Work supported in part by FWF, OEAW, and NASA.

Diatom production in the marine environment : implications for larval fish growth and condition

DEFF Research Database (Denmark)

St. John, Michael; Clemmesen, C.; Lund, T.

2001-01-01

To test the effects of diatom production on larval fish growth and condition. laboratory experiments were performed with larval North Sea cod reared on different algal food chains. These food chains were based on cultures of (a) the diatoms Skeletonema costatum and Thalassiosira weissflogii: (b....../omega6 fatty acids in the algal source had no significant effect. The highest and lowest growth rates were observed in food chains based on H. triquetra and T. weissflogii. respectively (means for days 14-16 of 4.0 and - 4.7). The mixed diatom/dinoflagellate diet resulted in inter- mediate growth rates...... and condition. Regressions of growth rates against EPA and DHA content indicated no inhibitory effect of diatom production on growth in larval cod...

SORPTION OF Cu2+ IONS ONTO DIATOMITE CONSTITUENTS

Directory of Open Access Journals (Sweden)

Vasile Rusu

2009-06-01

Full Text Available Studies of the sorption capacity towards Cu2+ ions of diatomite from the Ghidirim location of RM, as well as of the extracted clay phase are presented. Separated clay fraction from diatomic material is clean enough, and especially is rich in montmorillonite. Maximum sorption capacity for studied clay fraction is achieved by rising the temperature of calcination treatment up to 200oC. At higher temperatures the lattice of montmorillonite is contracted and its sorption capacity towards Cu2+ ions decreases strongly.

Possibility of gas sensor based on C_2_0 molecular devices

International Nuclear Information System (INIS)

Zhao, Wenkai; Yang, Chuanlu; Zou, Dongqing; Sun, Zhaopeng; Ji, Guomin

2017-01-01

We theoretically investigate the possibility of diatomic gas detection (NO, CO, O_2) by making use of the transport properties of the C_2_0 molecular junctions. The calculations are performed by using nonequilibrium Green's function (NEGF) formalism in combination with density functional theory (DFT). In this work, we systematically study the most stable adsorption structural configurations, adsorption energy, and the transport properties on C_2_0 molecular junctions with these diatomic gas molecules. It is found that NO and O_2 gas molecule can be detected selectively. We suggest its possibility of nanosensors for highly sensitive and selective based on C_2_0 molecular junction systems. - Highlights: • The most favorable adsorption site is investigated. • The mechanism of gas sensors is revealed. • NO and O_2 gas molecules can be detected by C_2_0 selectively.

Shared Epizoic Taxa and Differences in Diatom Community Structure Between Green Turtles (Chelonia mydas) from Distant Habitats.

Science.gov (United States)

Majewska, Roksana; de Vijver, Bart Van; Nasrolahi, Ali; Ehsanpour, Maryam; Afkhami, Majid; Bolaños, Federico; Iamunno, Franco; Santoro, Mario; De Stefano, Mario

2017-11-01

The first reports of diatoms growing on marine mammals date back to the early 1900s. However, only recently has direct evidence been provided for similar associations between diatoms and sea turtles. We present a comparison of diatom communities inhabiting carapaces of green turtles Chelonia mydas sampled at two remote sites located within the Indian (Iran) and Atlantic (Costa Rica) Ocean basins. Diatom observations and counts were carried out using scanning electron microscopy. Techniques involving critical point drying enabled observations of diatoms and other microepibionts still attached to sea turtle carapace and revealed specific aspects of the epizoic community structure. Species-poor, well-developed diatom communities were found on all examined sea turtles. Significant differences between the two host sea turtle populations were observed in terms of diatom abundance and their community structure (including growth form structure). A total of 12 and 22 diatom taxa were found from sea turtles in Iran and Costa Rica, respectively, and eight of these species belonging to Amphora, Chelonicola, Cocconeis, Navicula, Nitzschia and Poulinea genera were observed in samples from both locations. Potential mechanisms of diatom dispersal and the influence of the external environment, sea turtle behaviour, its life stage, and foraging and breeding habitats, as well as epibiotic bacterial flora on epizoic communities, are discussed.

Exploring Ion-Ion Interactions in Aqueous Solutions by a Combination of Molecular Dynamics and Neutron Scattering

Czech Academy of Sciences Publication Activity Database

Kohagen, Miriam; Pluhařová, E.; Mason, Philip E.; Jungwirth, Pavel

2015-01-01

Roč. 6, č. 9 (2015), s. 1563-1567 ISSN 1948-7185 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : ion pairing * molecular dynamics * neutron scattering Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 8.539, year: 2015 http://pubs.acs.org/doi/pdf/10.1021/acs.jpclett.5b00060

Molecular Characterization of CTR-type Copper Transporters in an Oceanic Diatom, Thalassiosira oceanica 1005

Science.gov (United States)

Kong, L.; Price, N. M.

2016-02-01

Copper is an essential micronutrient for phytoplankton growth because of its role as a redox cofactor in electron transfer proteins in photosynthesis and respiration, and a potentially limiting resource in parts of the open sea. Thalassiosira oceanica 1005 can grow at inorganic copper concentrations varying from 10 fmol/L to 10 nmol/L by regulating copper uptake across plasma membrane. Four putative CTR-type copper transporter genes (ToCTR1, ToCTR2, ToCTR3.1 and ToCTR3.2) were identified by BLASTP search against the T. oceanica genome. Predicted gene models were revised by assembled mRNA sequencing transcripts and updated gene models contained all conserved features of characterized CTR-type copper transporters. ToCTR3.1 and ToCTR3.2 may arise from one another by gene duplication as they shared a sequence similarity of 97.6% with a peptide insertion of 5 amino acids at N-terminus of ToCTR3.1. The expression of ToCTR1, ToCTR2 and ToCTR3.1/3.2 was upregulated in low copper concentrations, but only ToCTR3.1/3.2 showed a significant increase (2.5 fold) in copper-starved cells. Both ToCTR3.1 and ToCTR3.2 restored growth of a yeast double mutant, Saccharomyces cerevisiae ctr1Δctr3Δ, in copper deficient medium. GFP-fused ToCTR expression showed that some ToCTR3.1 localized to the plasma membrane but a large portion was retained in the endoplasmic reticulum. Inefficient targeting of ToCTR3.1 to the yeast outer membrane may explain poorer growth compared to the Saccharomyces native ScCTR1 transformant. Thus, diatom CTR genes encoding CTR-type copper transporters show high-affinity copper uptake and their regulation may enable diatoms to survive in ocean environments containing a wide range of copper concentrations.

The influence of land use on water quality and diatom community ...

African Journals Online (AJOL)

Epilithic diatom communities offer a holistic and integrated approach for assessing water quality as they remain in one place for a number of months and reflect an ecological memory of water quality over a period of time. The objective of this study is to use diatom assemblages to distinguish between particular land types ...

Photosynthetic Pigments in Diatoms

OpenAIRE

Kuczynska, Paulina; Jemiola-Rzeminska, Malgorzata; Strzalka, Kazimierz

2015-01-01

Photosynthetic pigments are bioactive compounds of great importance for the food, cosmetic, and pharmaceutical industries. They are not only responsible for capturing solar energy to carry out photosynthesis, but also play a role in photoprotective processes and display antioxidant activity, all of which contribute to effective biomass and oxygen production. Diatoms are organisms of a distinct pigment composition, substantially different from that present in plants. Apart from light-harvestin...

Mobility and molecular ions of dimethyl methyl phosphonate, methyl salicylate and acetone

Science.gov (United States)

Nowak, D. M.

1983-06-01

The mobilities of positive and negative reactant ions are reported for (H2O)nH(+); (H2O)2O2 and (H2O)2CO3(-) ion clusters. The formation of positive DMMP monomer and dimer is reported, and equilbria molecular reactions are reported. Acetone is reported as forming a dimer at 81 ppb with a reduced mobility (K sub o) of 1.82, Methyl salicylate is shown to form a protonated and hydrated positive monomer. Mixtures of DMMP and methyl salicylate with acetone showed a substantial change in DMMP ion clustering and little or no change in the methyl salicylate mobility spectra. Negative ions were not observed for DMMP, methyl salicylate, acetone and the mixtures under the conditions reported.

Three-dimensional densitometry imaging of diatom cells using STIM tomography

International Nuclear Information System (INIS)

Habchi, C.; Nguyen, D.T.; Deves, G.; Incerti, S.; Lemelle, L.; Van Vang, P. Le; Moretto, Ph.; Ortega, R.; Seznec, H.; Sakellariou, A.; Sergeant, C.; Simionovici, A.; Ynsa, M.D.; Gontier, E.; Heiss, M.; Pouthier, T.; Boudou, A.; Rebillat, F.

2006-01-01

Scanning transmission ion microscopy tomography (STIM-T) was carried out on diatom cells with the aim of displaying their 3D structure and performing density measurements on their silica skeleton. Two software packages were compared for data reduction: TomoRebuild, based on a simple filtered backprojection algorithm, and DISRA, an iterative program. Silicon carbide microfibres of known density were also analysed as reference specimens. Similar results were obtained with both algorithms, demonstrating the ability of STIM-T to provide density measurements at the cell level without requiring any standard calibration samples. This unique feature stresses the interest of STIM-T to accurately normalise X ray emission micro-tomography data from synchrotron radiation (SXRF: synchrotron radiation X-ray fluorescence) or ion beam sources (PIXE: particle induced X-ray emission). Possible enhancements of the DISRA code are discussed in order to facilitate its use for the reconstruction of future PIXE/STIM tomography data. A 'nanoprobe' coupled to a Singletron[reg] accelerator, allowing a spatial resolution of a few tens of nanometers, is going to be built in the coming months at the Centre d'Etudes Nucleaires de Bordeaux Gradignan (CENBG). This new facility will bring promising applications in imaging and analysis at the sub-cellular level

Dissociative recombination of the CH+ molecular ion at low energy

Science.gov (United States)

Chakrabarti, K.; Mezei, J. Zs; Motapon, O.; Faure, A.; Dulieu, O.; Hassouni, K.; Schneider, I. F.

2018-05-01

The reactive collision of the CH+ molecular ion with an electron is studied in the framework of the multichannel quantum defect theory, taking into account the contribution of the core-excited Rydberg states. In addition to the X 1Σ+ ground state of the ion, we also consider the contribution to the dynamics of the a 3Π and A 1Π excited states of CH+. Our results—in the case of the dissociative recombination in good agreement with the storage ring measurements—rely on decisive improvements—complete account of the ionisation channels and accurate evaluation of the reaction matrix—of a previously used model.

Studies on fouling diatoms from the Zuari Estuary, Goa (west coast of India)

Digital Repository Service at National Institute of Oceanography (India)

Redekar, P.D.; Wagh, A.B.

from offshore waters of Bombay High area using aluminium panels and recorded 58 species of fouling diatoms Of these Navicula Coscinodiscus Rhizosolenia and Chaetoceros were found to be common The dominance of Centrales over Pennales in water column... on fouling diatoms from the Zuari estuary, Goa (West coast of India) 119 Pangu (1993) used mild steel, aluminium, fiberglass and glass test panels and the immersion period of panels was long (1 month to 11 months) The fouling diatoms from Waghotana...

Ocean acidification modulates expression of genes and physiological performance of a marine diatom

Science.gov (United States)

Li, Y.; Zhuang, S.; Wu, Y.; Ren, H.; Cheng, F.; Lin, X.; Wang, K.; Beardall, J.; Gao, K.

2015-09-01

Ocean Acidification (OA) is known to affect various aspects of the physiological performance of diatoms, but there is little information on the underlining molecular mechanisms involved. Here, we show that in the model diatom Phaeodactylum tricornutum expression of the genes related to light harvesting, carbon acquisition and carboxylation, nitrite assimilation and ATP synthesis are modulated by OA. Growth and photosynthetic carbon fixation were enhanced by elevated CO2 (1000 μatm) under both constant indoor and fluctuating outdoor light regimes. The genetic expression of nitrite reductase (NiR) was up-regulated by OA regardless of light levels and/or regimes. The transcriptional expression of fucoxanthin chlorophyll a/c protein (lhcf type (FCP)) and mitochondrial ATP synthase (mtATP synthase) genes were also enhanced by OA, but only under high light intensity. OA treatment decreased the expression of β-carbonic anhydrase (β-CA) along with down-regulation of CO2 concentrating mechanisms (CCMs). Additionally, the genes for these proteins (NiR, FCP, mtATP synthase, β-CA) showed diel expressions either under constant indoor light or fluctuating sunlight. Thus, OA enhanced photosynthetic and growth rates by stimulating nitrogen assimilation and indirectly by down-regulating the energy-costly inorganic carbon acquisition process.

Impact of marine influence and cultivation on the diatom flora of ...

African Journals Online (AJOL)

During a limnological and palaeolimnological study of the western part of the Great Coast of Senegal, an analysis of diatoms was carried out in Thiaroye Pond in the suburbs of Dakar. Current diatom flora in the water and on floating plants, and subfossil flora in two cores were sampled in 1996 and 2003. A total of 104 ...

Contribution to the Study of the flora diatomic Nahr Yahfufah (Lebanon)

International Nuclear Information System (INIS)

SLIM, K.; ALOUF, N.

1984-01-01

Contribution to the study of Diatomic flora on Nahr Yahfufah Lebanon. From October 1980 to June 1982 a hydrobiologic study has taken place on the river of Yahfufah situated to the west of anti Lebanon. From the diatomic population 52 species and varieties were designated. Further more the physico-chemical parameters were followed and studied. (author).

External-field shifts in precision spectroscopy of hydrogen molecular ions

Energy Technology Data Exchange (ETDEWEB)

Bakalov, Dimitar, E-mail: dbakalov@inrne.bas.bg [INRNE, Bulgarian Academy of Sciences (Bulgaria); Korobov, Vladimir [Joint Institute for Nuclear Research (Russian Federation); Schiller, Stephan [Heinrich-Heine-Universitat Dusseldorf, Institut fur Experimentalphysik (Germany)

2015-08-15

The Effective Hamiltonian of the hydrogen molecular ions is a convenient tool for the evaluation of the shift of the energy levels of the ro-vibrational states and the frequencies of the transitions between them, due to external electric and magnetic fields. Using the Effective Hamiltonian, composite frequencies of suppressed susceptibility to external fields are constructed.

An improved coupled-states approximation including the nearest neighbor Coriolis couplings for diatom-diatom inelastic collision

Science.gov (United States)

Yang, Dongzheng; Hu, Xixi; Zhang, Dong H.; Xie, Daiqian

2018-02-01

Solving the time-independent close coupling equations of a diatom-diatom inelastic collision system by using the rigorous close-coupling approach is numerically difficult because of its expensive matrix manipulation. The coupled-states approximation decouples the centrifugal matrix by neglecting the important Coriolis couplings completely. In this work, a new approximation method based on the coupled-states approximation is presented and applied to time-independent quantum dynamic calculations. This approach only considers the most important Coriolis coupling with the nearest neighbors and ignores weaker Coriolis couplings with farther K channels. As a result, it reduces the computational costs without a significant loss of accuracy. Numerical tests for para-H2+ortho-H2 and para-H2+HD inelastic collision were carried out and the results showed that the improved method dramatically reduces the errors due to the neglect of the Coriolis couplings in the coupled-states approximation. This strategy should be useful in quantum dynamics of other systems.

Diatom community dynamics in a tropical, monsoon-influenced environment: West coast of India

Digital Repository Service at National Institute of Oceanography (India)

DeCosta, P.M.; Anil, A.C.

Diatom communities are influenced by environmental perturbations, such as the monsoon system that impact the niche opportunities of species. To discern the influence of the monsoon system on diatom community structure, we sampled during two...

Development of a diatom-based multimetric index for acid mine drainage impacted depressional wetlands.

Science.gov (United States)

Riato, Luisa; Leira, Manel; Della Bella, Valentina; Oberholster, Paul J

2018-01-15

Acid mine drainage (AMD) from coal mining in the Mpumalanga Highveld region of South Africa has caused severe chemical and biological degradation of aquatic habitats, specifically depressional wetlands, as mines use these wetlands for storage of AMD. Diatom-based multimetric indices (MMIs) to assess wetland condition have mostly been developed to assess agricultural and urban land use impacts. No diatom MMI of wetland condition has been developed to assess AMD impacts related to mining activities. Previous approaches to diatom-based MMI development in wetlands have not accounted for natural variability. Natural variability among depressional wetlands may influence the accuracy of MMIs. Epiphytic diatom MMIs sensitive to AMD were developed for a range of depressional wetland types to account for natural variation in biological metrics. For this, we classified wetland types based on diatom typologies. A range of 4-15 final metrics were selected from a pool of ~140 candidate metrics to develop the MMIs based on their: (1) broad range, (2) high separation power and (3) low correlation among metrics. Final metrics were selected from three categories: similarity to reference sites, functional groups, and taxonomic composition, which represent different aspects of diatom assemblage structure and function. MMI performances were evaluated according to their precision in distinguishing reference sites, responsiveness to discriminate reference and disturbed sites, sensitivity to human disturbances and relevancy to AMD-related stressors. Each MMI showed excellent discriminatory power, whether or not it accounted for natural variation. However, accounting for variation by grouping sites based on diatom typologies improved overall performance of MMIs. Our study highlights the usefulness of diatom-based metrics and provides a model for the biological assessment of depressional wetland condition in South Africa and elsewhere. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular dynamics simulation study of the "stay or leave" problem for two magnesium ions in gene transcription.

Science.gov (United States)

Wu, Shaogui

2017-06-01

Two magnesium ions play important roles in nucleotide addition cycle (NAC) of gene transcription. However, at the end of each NAC, why does one ion stay in the active site while the other ion leaves with product pyrophosphate (PP i )? This problem still remains obscure. In this work, we studied the problem using all-atom molecular dynamics simulation combined with steered molecular dynamics and umbrella sampling simulation methods. Our simulations reveal that although both ions are located in the active site after chemistry, their detailed positions are not symmetrical, leading to their different forces from surrounding groups. One ion makes weaker contacts with PP i than the whole protein. Hence, PP i release is less likely to take it away. The other one forms tighter contacts with PP i relative to the protein. The formed (Mg 2+ -PP i ) 2- complex is found to break the contacts with surrounding protein residues one by one so as to dissociate from the active site. This effectively avoids the coexistence of two ions in the active site after PP i release and guarantees a reasonable Mg 2+ ion number in the active site for the next NAC. The observations from this work can provide valuable information for comprehensively understanding the molecular mechanism of transcription. Proteins 2017; 85:1002-1007. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Vector properties in molecular photodissociation

International Nuclear Information System (INIS)

Underwood, J.

1999-12-01

The technique of resonance enhanced multi-photon ionization (REMPI) of atomic and molecular species produced from a photofragmentation event combined with time-of flight (TOF) detection is used to examine scalar and vector properties following photodissociation. This technique is applied to the study of methyl bromide dissociation in a product state specific manner. We report measurements of the angular distributions and kinetic energy releases of the resulting bromine atoms in the ground and first spin-orbit excited state. Additionally we report measurements of the angular distributions and kinetic energy releases of the methyl fragment in the ground vibrational state, and also the excited state with one quanta in the ν 2 vibrational modes. These studies were carried out in the red wing of the absorption band at several wavelengths. For these measurements we were able to resolve the spin orbit state of the partner bromine fragment. From our observations we find new evidence for enhanced nonadiabatic curve crossing active in methyl bromide dissociation in comparison with earlier studies of methyl iodide. The atomic polarization produced following photodissociation of a diatomic molecule was investigated both theoretically and experimentally. We develop theoretical expressions relating the lab frame and molecular frame atomic polarization to the photoexcitation and subsequent dissociation of a diatomic molecule. This treatment includes both incoherent, coherent and non-adiabatic processes which may be active in the photodissociation process. We treat the general case of a polarized diatomic molecule yielding two fragments with non zero angular momentum. Experimentally, an investigation of the polarization of atomic Cl( 2 P 3/2 ) photofragments from the ∼330 nm photolysis of molecular chlorine using the REMPI-TOF technique is reported. We present a theoretical framework in which to treat such experiments allowing the extraction of parameters with direct physical

Genetic and physiological responses of three freshwater diatoms to realistic diuron exposures.

Science.gov (United States)

Moisset, S; Kim Tiam, S; Feurtet-Mazel, A; Morin, S; Delmas, F; Mazzella, N; Gonzalez, P

2015-03-01

This study examined the effects of diuron on strains of three major freshwater diatom species, Eolimna minima, Nitzschia palea and Planothidium lanceolatum. These species are frequently recorded in the Morcille River, where diuron runs off during phytosanitary treatments of the vineyards around. Here, there were three diatom exposure groups for each species: 0, 1 and 10 μg/L diuron during a 14-day laboratory assessment. Diuron water concentration, cell number, photosynthetic activity and gene expression were assessed at 6 h and 2, 7 and 14 days after contamination. Diuron exposure altered photosynthetic activity in that the optimal quantum yield of photosystem II (PSII) decreased between 40 and 50% and, for P. lanceolatum at 10 μg/L, there was complete inhibition. Genetic responses indicated diuron effects on both photosystem II and mitochondrial metabolism in all three species at both diuron exposure levels. Thus, analysis of the expression of psaA, d1, cox1, nad5 and 12s could be an early biomarker to detect pesticide pollution. Overall, this study revealed differences in diuron sensitivity among the three species: E. minima and N. palea appeared to be more tolerant than P. lanceolatum. These results suggest that the development of molecular tools, and more precisely of biomarkers, will aid in early assessment of contamination and water quality.

Diatom stratigraphy and long-term dissolved silica concentrations in the Baltic Sea

Science.gov (United States)

Olli, Kalle; Clarke, Annemarie; Danielsson, Åsa; Aigars, Juris; Conley, Daniel J.; Tamminen, Timo

2008-10-01

In many parts of the world coastal waters with anthropogenic eutrophication have experienced a gradual depletion of dissolved silica (DSi) stocks. This could put pressure on spring bloom diatom populations, e.g. by limiting the intensity of blooms or by causing shifts in species composition. In addition, eutrophication driven enhanced diatom growth is responsible for the redistribution of DSi from the water phase to the sediments, and changes in the growth conditions may be reflected in the sediment diatom stratigraphy. To test for changes in diatom communities we have analyzed four sediment cores from the Baltic Sea covering approximately the last 100 years. The sediment cores originate from the western Gulf of Finland, the Kattegat, the Baltic Proper and the Gulf of Riga. Three out of the four cores reveal only minor changes in composition of diatom assemblages, while the Gulf of Riga core contains major changes, occurring after the second World War. This area is set apart from the other Baltic Sea basins by a high frequency of low after spring bloom DSi concentrations (< 2 µmol L - 1 ) during a relatively well defined time period from 1991-1998. In 1991 to 1993 a rapid decline of DSi spring concentrations and winter stocks (down to 5 µmol L - 1 ) in the Gulf was preceded by exceptionally intense diatom spring blooms dominated by the heavily silicified species Thalassiosira baltica (1991-1992; up to 5.5 mg ww L - 1 ). T. baltica has been the principal spring bloom diatom in the Gulf of Riga since records began in 1975. DSi consumption and biomass yield experiments with cultured T. baltica suggest that intense blooms can potentially exhaust the DSi stock of the water column and exceed the annual Si dissolution in the Gulf of Riga. The phytoplankton time series reveals another exceptional T. baltica bloom period in 1981-1983 (up to 8 mg L - 1 ), which, however, took place before the regular DSi measurements. These periods may be reflected in the conspicuous

Epibiotic Diatoms Are Universally Present on All Sea Turtle Species

OpenAIRE

Robinson, Nathan J.; Majewska, Roksana; Lazo-Wasem, Eric A.; Nel, Ronel; Paladino, Frank V.; Rojas, Lourdes; Zardus, John D.; Pinou, Theodora

2016-01-01

The macro-epibiotic communities of sea turtles have been subject to growing interest in recent years, yet their micro-epibiotic counterparts are almost entirely unknown. Here, we provide the first evidence that diatoms are epibionts for all seven extant species of sea turtle. Using Scanning Electron Microscopy, we inspected superficial carapace or skin samples from a single representative of each turtle species. We distinguished 18 diatom taxa from these seven individuals, with each sea turtl...

Biological monitoring of lotic ecosystems: the role of diatoms.

Science.gov (United States)

Bere, T; Tundisi, J G

2010-08-01

Increasing anthropogenic influence on lotic environments as a result of civilisation has captured public interest because of the consequent problems associated with deterioration of water quality. Various biological monitoring methods that provide a direct measure of ecological integrity by using the response of biota to environmental changes have been developed to monitor the ecological status of lotic environments. Diatoms have been used extensively in this regard and this review attempts to summarise the basic concepts associated with biological monitoring using benthic diatoms. Where possible, examples from work carried out in Brazil are used.

Rotation-vibrational spectra of diatomic molecules and nuclei with Davidson interactions

CERN Document Server

Rowe, D J

1998-01-01

Complete rotation-vibrational spectra and electromagnetic transition rates are obtained for Hamiltonians of diatomic molecules and nuclei with Davidson interactions. Analytical results are derived by dynamical symmetry methods for diatomic molecules and a liquid-drop model of the nucleus. Numerical solutions are obtained for a many-particle nucleus with quadrupole Davidson interactions within the framework of the microscopic symplectic model. (author)

Functional Annotation of Ion Channel Structures by Molecular Simulation.

Science.gov (United States)

Trick, Jemma L; Chelvaniththilan, Sivapalan; Klesse, Gianni; Aryal, Prafulla; Wallace, E Jayne; Tucker, Stephen J; Sansom, Mark S P

2016-12-06

Ion channels play key roles in cell membranes, and recent advances are yielding an increasing number of structures. However, their functional relevance is often unclear and better tools are required for their functional annotation. In sub-nanometer pores such as ion channels, hydrophobic gating has been shown to promote dewetting to produce a functionally closed (i.e., non-conductive) state. Using the serotonin receptor (5-HT 3 R) structure as an example, we demonstrate the use of molecular dynamics to aid the functional annotation of channel structures via simulation of the behavior of water within the pore. Three increasingly complex simulation analyses are described: water equilibrium densities; single-ion free-energy profiles; and computational electrophysiology. All three approaches correctly predict the 5-HT 3 R crystal structure to represent a functionally closed (i.e., non-conductive) state. We also illustrate the application of water equilibrium density simulations to annotate different conformational states of a glycine receptor. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Dinoflagellate blooms in upwelling systems: Seeding, variability, and contrasts with diatom bloom behaviour

Science.gov (United States)

Smayda, T. J.; Trainer, V. L.

2010-04-01

The influence of diatom bloom behaviour, dinoflagellate life cycles, propagule type and upwelling bloom cycles on the seeding of dinoflagellate blooms in eastern boundary current upwelling systems is evaluated. Winter-spring diatom bloom behaviour is contrasted with upwelling bloom behaviour because their phenology impacts dinoflagellate blooms. The winter-spring diatom bloom is usually sustained, whereas the classical upwelling diatom bloom occurs as a series of separate, recurrent mini-blooms intercalated by upwelling-relaxation periods, during which dinoflagellates often bloom. Four sequential wind-regulated phases characterize upwelling cycles, with each phase having different effects on diatom and dinoflagellate bloom behaviour: bloom “spin up”, bloom maximum, bloom “spin down”, and upwelling relaxation. The spin up - bloom maximum is the period of heightened diatom growth; the spin down - upwelling-relaxation phases are the periods when dinoflagellates often bloom. The duration, intensity and ratio of the upwelling and relaxation periods making up upwelling cycles determine the potential for dinoflagellate blooms to develop within a given upwelling cycle and prior to the subsequent “spin up” of upwelling that favours diatom blooms. Upwelling diatoms and meroplanktonic dinoflagellates have three types of propagules available to seed blooms: vegetative cells, resting cells and resting cysts. However, most upwelling dinoflagellates are holoplanktonic, which indicates that the capacity to form resting cysts is not an absolute requirement for growth and survival in upwelling systems. The long-term (decadal) gaps in bloom behaviour of Gymnodinium catenatum and Lingulodinium polyedrum, and the unpredictable bloom behaviour of dinoflagellates generally, are examined from the perspective of seeding strategies. Mismatches between observed and expected in situ bloom behaviour and resting cyst dynamics are common among upwelling dinoflagellates. This

Accumulation of {sup 241}Am by suspended matter, diatoms and aquatic weeds of the Yenisei River

Energy Technology Data Exchange (ETDEWEB)

Zotina, T.A., E-mail: t_zotina@ibp.r [Institute of Biophysics SB RAS, Akademgorodok, Krasnoyarsk 660036 (Russian Federation); Bolsunovsky, A.Ya.; Bondareva, L.G. [Institute of Biophysics SB RAS, Akademgorodok, Krasnoyarsk 660036 (Russian Federation)

2010-02-15

In this work we experimentally estimated the capacities of the key components of the Yenisei River (Russia): particulate suspended matter (seston), diatom microalgae, and submerged macrophytes for accumulating {sup 241}Am from water. In our experiments large particles of seston (>8 mum), comparable in size with diatoms, took up most of americium from water. The accumulation of americium by isolated diatom algae (Asterionella formosa and Diatoma vulgare) was lower than by total seston. The concentration factors (CFs) of {sup 241}Am for seston of the Yenisei River in our experiments were (2.8-6.9).10{sup 5}; for diatoms - (1.5-4.2).10{sup 4}. The CFs for aquatic plant Elodea canadensis were within the same order of magnitude as those for diatoms. Activity concentration and CFs of {sup 241}Am were nearly the same in experiments under dark and light conditions. This is indicative of an energy independent mechanism of americium uptake from the water by diatoms and submerged macrophytes.

Anaerobic Nitrogen Turnover by Sinking Diatom Aggregates at Varying Ambient Oxygen Levels

Directory of Open Access Journals (Sweden)

Peter eStief

2016-02-01

Full Text Available In the world’s oceans, even relatively low oxygen (O2 levels inhibit anaerobic nitrogen cycling by free-living microbes. Sinking organic aggregates, however, might provide oxygen-depleted microbial hotspots in otherwise oxygenated surface waters. Here we show that sinking diatom aggregates can host anaerobic nitrogen cycling at ambient O2 levels well above the hypoxic threshold. Aggregates were produced from the ubiquitous diatom Skeletonema marinoi and the natural microbial community of seawater. Microsensor profiling through the center of sinking aggregates revealed internal anoxia at ambient 40% air saturation (~100 µmol O2 L-1 and below. Accordingly, anaerobic nitrate turnover inside the aggregates was evident within this range of ambient O2 levels. In incubations with 15N-labeled nitrate, individual Skeletonema aggregates produced NO2- (up to 10.7 nmol N h-1 per aggregate, N2 (up to 7.1 nmol N h-1, NH4+ (up to 2.0 nmol N h-1, and N2O (up to 0.2 nmol N h-1. Intriguingly, nitrate stored inside the diatom cells served as an additional, internal nitrate source for N2 production, which may partially uncouple anaerobic nitrate turnover by diatom aggregates from direct ambient nitrate supply. Sinking diatom aggregates can contribute directly to fixed-nitrogen loss in low-oxygen environments in the ocean and vastly expand the ocean volume in which anaerobic nitrogen turnover is possible, despite relatively high ambient O2 levels. Depending on the extent of intracellular nitrate consumption during the sinking process, diatom aggregates may also be involved in the long-distance export of nitrate to the deep ocean.

A stress surveillance system based on calcium and nitric oxide in marine diatoms.

Directory of Open Access Journals (Sweden)

Assaf Vardi

2006-03-01

Full Text Available Diatoms are an important group of eukaryotic phytoplankton, responsible for about 20% of global primary productivity. Study of the functional role of chemical signaling within phytoplankton assemblages is still in its infancy although recent reports in diatoms suggest the existence of chemical-based defense strategies. Here, we demonstrate how the accurate perception of diatom-derived reactive aldehydes can determine cell fate in diatoms. In particular, the aldehyde (2E,4E/Z-decadienal (DD can trigger intracellular calcium transients and the generation of nitric oxide (NO by a calcium-dependent NO synthase-like activity, which results in cell death. However, pretreatment of cells with sublethal doses of aldehyde can induce resistance to subsequent lethal doses, which is reflected in an altered calcium signature and kinetics of NO production. We also present evidence for a DD-derived NO-based intercellular signaling system for the perception of stressed bystander cells. Based on these findings, we propose the existence of a sophisticated stress surveillance system in diatoms, which has important implications for understanding the cellular mechanisms responsible for acclimation versus death during phytoplankton bloom successions.

Molecular-beam epitaxial growth and ion-beam analysis systems for functional materials research

International Nuclear Information System (INIS)

Takeshita, H.; Aoki, Y.; Yamamoto, S.; Naramoto, H.

1992-01-01

Experimental systems for molecular beam epitaxial growth and ion beam analysis have been designed and constructed for the research of inorganic functional materials such as thin films and superlattices. (author)

USE OF DIATOMS TO ASSES WATER QUALITY OF ANTHROPOGENICALLY MODIFIED MATYSÓWKA STREAM

Directory of Open Access Journals (Sweden)

Teresa Noga

2013-04-01

Full Text Available Matysówka stream is small, under 6 km long watercourse, which is a right-bank tributary of Strug River. In 2009–2011studies on the subject of diversity of diatom communities using diatom indices IPS, GDI and TDI for water quality assessment were conducted. On the stream 271 diatom taxa were identified, among which: Achnanthidium minutissimum var. minutissimum, Navicula cryptotenella, N. gregaria, N. lanceolata, N. tripunctata, Nitzschia linearis, N. pusilla, N. recta, Planothidium frequentissimum, Rhoicosphenia abbreviata were the most frequent. Middle and lower section of Matysówka stream was characterized by increased concentrations of phosphates, nitrites, ammonium, total phosphorus and nitrogen, BOD5. On the basis of diatom indices IPS and GDI waters were characterized as III–IV quality classes, while the TDI index revealed the worst water quality classes (IV–V.

The exotic molecular ion H{sub 4}{sup 3+} in a strong magnetic field; El ion molecular exotico H{sub 4}{sup 3+} en un campo magnetico intenso

Energy Technology Data Exchange (ETDEWEB)

Olivares P, H. [ICN-UNAM, A.P. 70-543, 04510 Mexico D.F. (Mexico)]. e-mail: horop@nucleares.unam.mx

2006-07-01

Using the variational method, a detailed study of the lowest m = 0, -1 electronic states of the exotic molecular ion H3+{sub 4} in a strong magnetic field, in the linear symmetric configuration parallel to the direction of the magnetic field is carried out. A extended study of the 1{sigma}g ground state (J.C. Lopez and A.Turbiner, Phys. Rev A 62, 022510, 2000) was performed obtaining that the potential energy curve displays a sufficiently deep minimum for finite internuclear distances, indicating the possible existence of the molecular ion H{sub 4}{sup 3+}, for magnetic fields of strength B > {approx} 3 x 10{sup 13} G. It is demonstrated that the excited state 1{pi}{sub u}, can exist for a magnetic field B = 4.414 x 10{sup 13} G corresponding to the limit of applicability of the non-relativistic theory. (Author)

Possibility of gas sensor based on C{sub 20} molecular devices

Energy Technology Data Exchange (ETDEWEB)

Zhao, Wenkai [School of Physics and Optoelectronics Engineering, Ludong University, Yantai 264025 (China); Yang, Chuanlu, E-mail: yangchuanlu@126.com [School of Physics and Optoelectronics Engineering, Ludong University, Yantai 264025 (China); Zou, Dongqing [School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100 (China); Sun, Zhaopeng [School of Physics and Optoelectronics Engineering, Ludong University, Yantai 264025 (China); Ji, Guomin [Electrical and Computer Engineering, The University of Oklahoma, Norman, Tulsa, OK 74078 (United States)

2017-06-09

We theoretically investigate the possibility of diatomic gas detection (NO, CO, O{sub 2}) by making use of the transport properties of the C{sub 20} molecular junctions. The calculations are performed by using nonequilibrium Green's function (NEGF) formalism in combination with density functional theory (DFT). In this work, we systematically study the most stable adsorption structural configurations, adsorption energy, and the transport properties on C{sub 20} molecular junctions with these diatomic gas molecules. It is found that NO and O{sub 2} gas molecule can be detected selectively. We suggest its possibility of nanosensors for highly sensitive and selective based on C{sub 20} molecular junction systems. - Highlights: • The most favorable adsorption site is investigated. • The mechanism of gas sensors is revealed. • NO and O{sub 2} gas molecules can be detected by C{sub 20} selectively.

Cellular metabolic responses of the marine diatom Pseudo-nitzschia multiseries associated with cell wall formation.

Science.gov (United States)

Xu, Bin; Luo, Chun-Shan; Liang, Jun-Rong; Chen, Dan-Dan; Zhuo, Wen-Hao; Gao, Ya-Hui; Chen, Chang-Ping; Song, Si-Si

2014-08-01

In this study a comparative proteomics approach involving a mass spectrometric analysis of synchronized cells was employed to investigate the cellular-level metabolic mechanisms associated with siliceous cell wall formation in the pennate diatom Pseudo-nitzschia multiseries. Cultures of P. multiseries were synchronized using the silicate limitation method. Approximately 75% of cells were arrested at the G2+M phase of the cell cycle after 48 h of silicate starvation. The majority of cells progressed to new valve synthesis within 5h of silicon replenishment. We compared the proteome of P. multiseries at 0, 4, 5, and 6h of synchronization progress upon silicon replenishment using two-dimensional gel electrophoresis. Forty-eight differentially expressed protein spots were identified in abundance (greater than two-fold change; Pwall formation. The proteomic profile analysis suggests that P. multiseries most likely employs multiple synergistic biochemical mechanisms for cell wall formation. These results improve our understanding of the molecular mechanisms underlying silicon cell wall formation and enhance our understanding of the important role played by diatoms in silicon biogeochemical cycling. Copyright © 2013 Elsevier B.V. All rights reserved.

The sexual phase of the diatom Pseudo-nitzschia multistriata: cytological and time-lapse cinematography characterization.

Science.gov (United States)

Scalco, Eleonora; Amato, Alberto; Ferrante, Maria Immacolata; Montresor, Marina

2016-11-01

Pseudo-nitzschia is a thoroughly studied pennate diatom genus for ecological and biological reasons. Many species in this genus, including Pseudo-nitzschia multistriata, can produce domoic acid, a toxin responsible for amnesic shellfish poisoning. Physiological, phylogenetic and biological features of P. multistriata were studied extensively in the past. Life cycle stages, including the sexual phase, fundamental in diatoms to restore the maximum cell size and avoid miniaturization to death, have been well described for this species. P. multistriata is heterothallic; sexual reproduction is induced when strains of opposite mating type are mixed, and proceeds with cells producing two functionally anisogamous gametes each; however, detailed cytological information for this process is missing. By means of confocal laser scanning microscopy and nuclear staining, we followed the nuclear fate during meiosis, and using time-lapse cinematography, we timed every step of the sexual reproduction process from mate pairing to initial cell hatching. The present paper depicts cytological aspects during gametogenesis in P. multistriata, shedding light on the chloroplast behaviour during sexual reproduction, finely describing the timing of the sexual phases and providing reference data for further studies on the molecular control of this fundamental process.

Molecular desorption of stainless steel vacuum chambers irradiated with 4.2  MeV/u lead ions

Directory of Open Access Journals (Sweden)

E. Mahner

2003-01-01

Full Text Available In preparation for the heavy ion program of the Large Hadron Collider at CERN, accumulation and cooling tests with lead ion beams have been performed in the Low Energy Antiproton Ring. These tests have revealed that due to the unexpected large outgassing of the vacuum system, the dynamic pressure of the ring could not be maintained low enough to reach the required beam intensities. To determine the actions necessary to lower the dynamic pressure rise, an experimental program has been initiated for measuring the molecular desorption yields of stainless steel vacuum chambers by the impact of 4.2  MeV/u lead ions with the charge states +27 and +53. The test chambers were exposed either at grazing or at perpendicular incidence. Different surface treatments (glow discharges, nonevaporable getter coating are reported in terms of the molecular desorption yields for H_{2}, CH_{4}, CO, Ar, and CO_{2}. Unexpected large values of molecular yields per incident ion up to 2×10^{4} molecules/ion have been observed. The reduction of the ion-induced desorption yield due to continuous bombardment with lead ions (beam cleaning has been investigated for five different stainless steel vacuum chambers. The implications of these results for the vacuum system of the future Low Energy Ion Ring and possible remedies to reduce the vacuum degradation are discussed.

Genotoxicity of cadmium in marine diatom Chaetoceros tenuissimus using the alkaline Comet assay

Digital Repository Service at National Institute of Oceanography (India)

Desai, S.R.; Verlecar, X.N.; Nagarajappa; Goswami, U.

of Cd increased growth of the diatom decreased. Alkaline single-cell gel electrophoresis (Comet assay) method, which is highly sensitive in detection of DNA damage in eukaryotic cells, was used to observe genomic changes in marine diatom cells. DNA...

Diatoms of the jukskei-crocodile river system (transvaal, republic of South Africa): a preliminary check list

CSIR Research Space (South Africa)

Schoeman, FR

1982-01-01

Full Text Available : V & R Printers. SCHOEMAN, F. R., 1976. Diatom indicator groups in the assessment of water quality in the Jukskei-Crocodile River system (Transvaal, Republic of South Afri ca). J. Limnol. Soc. yth. Afr. 2: 21?24. SCHOEMAN, F. R., 1979. Diatoms... groups of diatom spe cies have been successfully used as an index of the quality of running waters (Lange-Bertalot, 1978a; 1979a; 1979b; Schoeman, 1976; 1979). However, the successful determination of water quality using diatoms as indicators...

Molecular depth profiling of trehalose using a C{sub 60} cluster ion beam

Energy Technology Data Exchange (ETDEWEB)

Wucher, Andreas [Department of Physics, University of Duisburg-Essen, D-47048 Duisburg (Germany)], E-mail: andreas.wucher@uni-due.de; Cheng Juan; Winograd, Nicholas [Department of Chemistry, Pennsylvania State University, University Park, PA 16802 (United States)

2008-12-15

Molecular depth profiling of organic overlayers was performed using a mass selected fullerene ion beam in conjunction with time-of-flight (TOF-SIMS) mass spectrometry. The characteristics of depth profiles acquired on a 300-nm trehalose film on Si were studied as a function of the impact kinetic energy and charge state of the C{sub 60} projectile ions. We find that the achieved depth resolution depends only weakly upon energy.

Automated identification and quantification of glycerophospholipid molecular species by multiple precursor ion scanning

DEFF Research Database (Denmark)

Ejsing, Christer S.; Duchoslav, Eva; Sampaio, Julio

2006-01-01

We report a method for the identification and quantification of glycerophospholipid molecular species that is based on the simultaneous automated acquisition and processing of 41 precursor ion spectra, specific for acyl anions of common fatty acids moieties and several lipid class-specific fragment...... of glycerophospholipids. The automated analysis of total lipid extracts was powered by a robotic nanoflow ion source and produced currently the most detailed description of the glycerophospholipidome....

Probing physics beyond the standard model in diatomic molecules

International Nuclear Information System (INIS)

Denis, M.

2017-01-01

Nowadays, the incompleteness of the Standard Model of particles (SM) is largely acknowledged. One of its most obvious shortcomings is the lack of explanation for the huge surplus of matter over antimatter in the universe, the so-called baryon asymmetry of the universe. New CP (charge conjugation and spatial parity) violations absent in the SM are assumed to be responsible for this asymmetry. Such a violation could be observed, in ordinary matter through a set of interactions violating both parity and time-reversal symmetries (P, T -odd) among which the preponderant ones are the electron Electric Dipole Moment (eEDM), the electron-nucleon scalar-pseudoscalar (enSPS) and the nuclear magnetic quadrupole moment (nMQM) interactions. Hence, an experimental evidence of a non-zero P, T -odd interaction constant would be a probe of this New Physics beyond the Standard Model. The calculation of the corresponding molecular parameters is performed by making use of an elaborate four-component relativistic configuration interaction approach in polar diatomic molecules containing an actinide, that are particularly adequate systems for eEDM experiments, such as ThO that allowed for assigning the most constraining upper bound on the eEDM and ThF"+ that will be used in a forthcoming experiment. Those results will be of crucial importance in the interpretation of the measurements since the fundamental constants can only be evaluated if one combines both experimental energy shift measurements and theoretical molecular parameters. This manuscript proceeds as follows, after an introduction to the general background of the search of CP-violations and its consequences for the understanding of the Universe (Chapter 1), a presentation of the underlying theory of the evidence of such violation in ordinary matter, namely the P, T -odd sources of the Electric Dipole Moment of a many-electron system, as well as the relevant molecular parameters is given in Chapter 2. A similar introduction to

Diatom. A potential bio-accumulator of gold

International Nuclear Information System (INIS)

Chakraborty, N.; Pal, R.; Ramaswami, A.; Nayak, D.; Lahiri, S.

2006-01-01

The bioaccumulation of gold in trace concentration by Nitzschia obtusa and Navicula minima, two members of bacillariophyceae, has been studied. It has been observed that Nitzschia obtusa showed better accumulation of gold in acidic pH in comparison to neutral and basic pH. Maximum accumulation was observed with 1 mg x kg -1 or less gold concentration. However, the accumulation by the living cells was reduced when the matrix concentration was higher. Navicula minima, on the other hand, found to be a better accumulator of gold in wide ranges of pH and substrate concentration of the media. It was also inferred that the gold accumulation by diatom was mainly due to adsorption by biosilica (siliceous frustules of dead diatom cells). Accumulated gold was recovered with conc. HNO 3 . (author)

IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels.

Directory of Open Access Journals (Sweden)

Kota Kasahara

Full Text Available Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering. This approach effectively revealed the ion conduction mechanisms and their dependence on the conditions, i.e., ion concentration and membrane voltage. Here, we present an easy-to-use computational toolkit for ion-binding state analysis, called IBiSA_tools. This toolkit consists of a C++ program and a series of Python and R scripts. From the trajectory file of MD simulations and a structure file, users can generate several images and statistics of ion conduction processes. A complex network named ion-binding state graph is generated in a standard graph format (graph modeling language; GML, which can be visualized by standard network analyzers such as Cytoscape. As a tutorial, a trajectory of a 50 ns MD simulation of the Kv1.2 channel is also distributed with the toolkit. Users can trace the entire process of ion-binding state analysis step by step. The novel method for analysis of ion conduction mechanisms of ion channels can be easily used by means of IBiSA_tools. This software is distributed under an open source license at the following URL: http://www.ritsumei.ac.jp/~ktkshr/ibisa_tools/.

Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability.

Science.gov (United States)

Marchetti, Adrian; Schruth, David M; Durkin, Colleen A; Parker, Micaela S; Kodner, Robin B; Berthiaume, Chris T; Morales, Rhonda; Allen, Andrew E; Armbrust, E Virginia

2012-02-07

In vast expanses of the oceans, growth of large phytoplankton such as diatoms is limited by iron availability. Diatoms respond almost immediately to the delivery of iron and rapidly compose the majority of phytoplankton biomass. The molecular bases underlying the subsistence of diatoms in iron-poor waters and the plankton community dynamics that follow iron resupply remain largely unknown. Here we use comparative metatranscriptomics to identify changes in gene expression associated with iron-stimulated growth of diatoms and other eukaryotic plankton. A microcosm iron-enrichment experiment using mixed-layer waters from the northeastern Pacific Ocean resulted in increased proportions of diatom transcripts and reduced proportions of transcripts from most other taxa within 98 h after iron addition. Hundreds of diatom genes were differentially expressed in the iron-enriched community compared with the iron-limited community; transcripts of diatom genes required for synthesis of photosynthesis and chlorophyll components, nitrate assimilation and the urea cycle, and synthesis of carbohydrate storage compounds were significantly overrepresented. Transcripts of genes encoding rhodopsins in eukaryotic phytoplankton were significantly underrepresented following iron enrichment, suggesting rhodopsins help cells cope with low-iron conditions. Oceanic diatoms appear to display a distinctive transcriptional response to iron enrichment that allows chemical reduction of available nitrogen and carbon sources along with a continued dependence on iron-free photosynthetic proteins rather than substituting for iron-containing functional equivalents present within their gene repertoire. This ability of diatoms to divert their newly acquired iron toward nitrate assimilation may underlie why diatoms consistently dominate iron enrichments in high-nitrate, low-chlorophyll regions.

Intracellular Nitrate of Marine Diatoms as a Driver of Anaerobic Nitrogen Cycling in Sinking Aggregates

Directory of Open Access Journals (Sweden)

Anja Kamp

2016-11-01

Full Text Available Diatom-bacteria aggregates are key for the vertical transport of organic carbon in the ocean. Sinking aggregates also represent pelagic microniches with intensified microbial activity, oxygen depletion in the center, and anaerobic nitrogen cycling. Since some of the aggregate-forming diatom species store nitrate intracellularly, we explored the fate of intracellular nitrate and its availability for microbial metabolism within anoxic diatom-bacteria aggregates. The ubiquitous nitrate-storing diatom Skeletonema marinoi was studied as both axenic cultures and laboratory-produced diatom-bacteria aggregates. Stable 15N isotope incubations under dark and anoxic conditions revealed that axenic S. marinoi is able to reduce intracellular nitrate to ammonium that is immediately excreted by the cells. When exposed to a light:dark cycle and oxic conditions, S. marinoi stored nitrate intracellularly in concentrations > 60 mmol L-1 both as free-living cells and associated to aggregates. Intracellular nitrate concentrations exceeded extracellular concentrations by three orders of magnitude. Intracellular nitrate was used up within 2-3 days after shifting diatom-bacteria aggregates to dark and anoxic conditions. Thirty-one percent of the diatom-derived nitrate was converted to nitrogen gas, indicating that a substantial fraction of the intracellular nitrate pool of S. marinoi becomes available to the aggregate-associated bacterial community. Only 5% of the intracellular nitrate was reduced to ammonium, while 59% was recovered as nitrite. Hence, aggregate-associated diatoms accumulate nitrate from the surrounding water and sustain complex nitrogen transformations, including loss of fixed nitrogen, in anoxic, pelagic microniches. Additionally, it may be expected that intracellular nitrate not converted before the aggregates have settled onto the seafloor could fuel benthic nitrogen transformations.

Large centric diatoms allocate more cellular nitrogen to photosynthesis to counter slower RUBISCO turnover rates

Directory of Open Access Journals (Sweden)

Yaping eWu

2014-12-01

Full Text Available Diatoms contribute ~40% of primary production in the modern ocean and encompass the largest cell size range of any phytoplankton group. Diatom cell size influences their nutrient uptake, photosynthetic light capture, carbon export efficiency, and growth responses to increasing pCO2. We therefore examined nitrogen resource allocations to the key protein complexes mediating photosynthesis across six marine centric diatoms, spanning 5 orders of magnitude in cell volume, under past, current and predicted future pCO2 levels, in balanced growth under nitrogen repletion. Membrane bound photosynthetic protein concentrations declined with cell volume in parallel with cellular concentrations of total protein, total nitrogen and chlorophyll. Larger diatom species, however, allocated a greater fraction (by 3.5 fold of their total cellular nitrogen to the soluble RUBISCO carbon fixation complex than did smaller species. Carbon assimilation per unit of RUBISCO large subunit (C RbcL-1 s-1 decreased with cell volume, from ~8 to ~2 C RbcL-1 s-1 from the smallest to the largest cells. Whilst a higher allocation of cellular nitrogen to RUBISCO in larger cells increases the burden upon their nitrogen metabolism, the higher RUBISCO allocation buffers their lower achieved RUBISCO turnover rate to enable larger diatoms to maintain carbon assimilation rates per total protein comparable to small diatoms. Individual species responded to increased pCO2, but cell size effects outweigh pCO2 responses across the diatom species size range examined. In large diatoms a higher nitrogen cost for RUBISCO exacerbates the higher nitrogen requirements associated with light absorption, so the metabolic cost to maintain photosynthesis is a cell size-dependent trait.

A finite difference Hartree-Fock program for atoms and diatomic molecules

Science.gov (United States)

Kobus, Jacek

2013-03-01

The newest version of the two-dimensional finite difference Hartree-Fock program for atoms and diatomic molecules is presented. This is an updated and extended version of the program published in this journal in 1996. It can be used to obtain reference, Hartree-Fock limit values of total energies and multipole moments for a wide range of diatomic molecules and their ions in order to calibrate existing and develop new basis sets, calculate (hyper)polarizabilities (αzz, βzzz, γzzzz, Az,zz, Bzz,zz) of atoms, homonuclear and heteronuclear diatomic molecules and their ions via the finite field method, perform DFT-type calculations using LDA or B88 exchange functionals and LYP or VWN correlations ones or the self-consistent multiplicative constant method, perform one-particle calculations with (smooth) Coulomb and Krammers-Henneberger potentials and take account of finite nucleus models. The program is easy to install and compile (tarball+configure+make) and can be used to perform calculations within double- or quadruple-precision arithmetic. Catalogue identifier: ADEB_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADEB_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 171196 No. of bytes in distributed program, including test data, etc.: 9481802 Distribution format: tar.gz Programming language: Fortran 77, C. Computer: any 32- or 64-bit platform. Operating system: Unix/Linux. RAM: Case dependent, from few MB to many GB Classification: 16.1. Catalogue identifier of previous version: ADEB_v1_0 Journal reference of previous version: Comput. Phys. Comm. 98(1996)346 Does the new version supersede the previous version?: Yes Nature of problem: The program finds virtually exact solutions of the Hartree-Fock and density functional theory type equations for atoms, diatomic molecules and their ions

Analytic vibrational matrix elements for diatomic molecules

International Nuclear Information System (INIS)

Bouanich, J.P.; Ogilvie, J.F.; Tipping, R.H.

1986-01-01

The vibrational matrix elements and expectation values for a diatomic molecule, including the rotational dependence, are calculated for powers of the reduced displacement in terms of the parameters of the Dunham potential-energy function. (orig.)

Molecular excitations: a new way to detect Dark Matter

Energy Technology Data Exchange (ETDEWEB)

Va' vra, J.

2014-09-01

We believe that the Dark Matter (DM) search should be expanded into the domain of detectors sensitive to molecular excitations, and so that we should create detectors which are more sensitive to collisions with very light WIMPs. In this paper we investigate in detail diatomic molecules, such as fused silica material with large OH-molecule content, and water molecules. Presently, we do not have suitable low-cost IR detectors to observe single photons, however some OH-molecular excitations extend to visible and UV wavelengths and can be measured by bialkali photocathodes. There are many other chemical substances with diatomic molecules, or more complex oil molecules, which could be also investigated. This idea invites searches in experiments having large target volumes of such materials coupled to a large array of single-photon detectors with bialkali or infrared-sensitive photocathodes.

Comparison between sedimentary and living diatoms in Lago Maggiore (N. Italy: implications of using transfer functions

Directory of Open Access Journals (Sweden)

Simona MUSAZZI

2001-02-01

Full Text Available We compared the recent history of living planktonic diatom assemblages in Lago Maggiore with the remains found in the topmost section of 14 sediment cores taken from the lake. Sediment samples showed a marked domination of planktonic taxa, but a significant proportion of benthic taxa was found in cores collected close to river mouths. Between-core variability in diatom assemblage and in diatom-inferred total phosphorus concentration was also estimated. The implications of our results for calibration data sets relating environmental variables to diatom assemblages are also discussed.

Diatomic gasdynamic lasers.

Science.gov (United States)

Mckenzie, R. L.

1972-01-01

Predictions from a numerical model of the vibrational relaxation of anharmonic diatomic oscillators in supersonic expansions are used to show the extent to which the small anharmonicity of gases like CO can cause significant overpopulations of upper vibrational states. When mixtures of CO and N2 are considered, radiative gain on many of the vibration-rotation transitions of CO is predicted. Experiments are described that qualitatively verify the predictions by demonstrating laser oscillation in CO-N2 expansions. The resulting CO-N2 gasdynamic laser displays performance characteristics that equal or exceed those of similar CO2 lasers.

Diatomic gasdynamic lasers

International Nuclear Information System (INIS)

McKenzie, R.L.

1971-12-01

Predictions from a numerical model of the vibrational relaxation of anharmonic diatomic oscillators in supersonic expansions are used to show the extent to which the small anharmonicity of gases like CO can cause significant over-populations of upper vibrational states. When mixtures of CO and N 2 are considered, radiative gain on many of the vibration-rotation transitions of CO is predicted. Experiments are described that qualitatively verify the predictions by demonstrating laser oscillation in CO-N 2 expansions. The resulting CO-N 2 gasdynamic laser displays performance characteristics that equal or exceed those of similar CO 2 lasers

A stress surveillance system based on calcium and nitric oxide in marine diatoms

NARCIS (Netherlands)

Vardi, A.; Formiggini, F.; Casotti, R.; De Martino, A.; Ribalet, F.; Miralto, A.; Bowler, C.

2006-01-01

Diatoms are an important group of eukaryotic phytoplankton, responsible for about 20% of global primary productivity. Study of the functional role of chemical signaling within phytoplankton assemblages is still in its infancy although recent reports in diatoms suggest the existence of chemical-based

A stress surveillance system based on calcium and nitric oxide in marine diatoms.

NARCIS (Netherlands)

Vardi, A.; Formiggini, F.; Casotti, R.; De Martino, A.; Ribalet, F.; Miralto, A.; Bowler, C.

2006-01-01

Diatoms are an important group of eukaryotic phytoplankton, responsible for about 20% of global primary productivity. Study of the functional role of chemical signaling within phytoplankton assemblages is still in its infancy although recent reports in diatoms suggest the existence of chemical-based

Diatom algae of the Guni river (Pamir)

International Nuclear Information System (INIS)

Kurbonova, P.A.; Hisoriev, H.H.

2006-01-01

There are presented the dates of the results of diatom algae (Bacillariophyta) of the Gunt river. There was found 107 species and 9 subspecies which belong to 3 classics, 12 ordos, 13 families and 28 genus

Spectrofluorometric and Molecular Modeling Studies on Binding of Nitrite Ion with Bovine Hemoglobin: Effect of Nitrite Ion on Amino Acid Residues

Science.gov (United States)

Madrakian, T.; Bagheri, H.; Afkhami, A.

2015-05-01

The interaction between nitrite ion and bovine hemoglobin was investigated by a spectrofluorometric technique. The experimental results indicated that the interaction causes a static quenching of the fluorescence of bovine hemoglobin, that the binding reaction is spontaneous, and that H-bonding interactions play a major role in binding of this ion to bovine hemoglobin. The formation constant for this interaction was calculated. Based on Förster's theory of nonradiative energy transfer, the binding distance between this ion and bovine hemoglobin was determined. Furthermore, the interaction of nitrite ion with tyrosine and tryptophan was investigated with synchronous fluorescence. There was no significant shift of the maximum emission wavelength with interactions of the mentioned ion with bovine hemoglobin, which implies that interaction of nitrite ion with bovine hemoglobin does not affect the microenvironment around the tryptophan and tyrosine residues. Furthermore, the effect of nitrite ion on amino acid residues of bovine hemoglobin was studied by a molecular docking technique.

Momentum autocorrelation function of a classic diatomic chain

Energy Technology Data Exchange (ETDEWEB)

Yu, Ming B., E-mail: mingbyu@gmail.com

2016-10-23

A classical harmonic diatomic chain is studied using the recurrence relations method. The momentum autocorrelation function results from contributions of acoustic and optical branches. By use of convolution theorem, analytical expressions for the acoustic and optical contributions are derived as even-order Bessel function expansions with coefficients given in terms of integrals of elliptic functions in real axis and a contour parallel to the imaginary axis, respectively. - Highlights: • Momentum autocorrelation function of a classic diatomic chain is studied. • It is derived as even-order Bessel function expansion using the convolution theorem. • The expansion coefficients are integrals of elliptic functions. • Addition theorem is used to reduce complex elliptic function to complex sum of real ones.

Molecular carbon nitride ion beams for enhanced corrosion resistance of stainless steel

Science.gov (United States)

Markwitz, A.; Kennedy, J.

2017-10-01

A novel approach is presented for molecular carbon nitride beams to coat stainless surfaces steel using conventional safe feeder gases and electrically conductive sputter targets for surface engineering with ion implantation technology. GNS Science's Penning type ion sources take advantage of the breaking up of ion species in the plasma to assemble novel combinations of ion species. To test this phenomenon for carbon nitride, mixtures of gases and sputter targets were used to probe for CN+ ions for simultaneous implantation into stainless steel. Results from mass analysed ion beams show that CN+ and a variety of other ion species such as CNH+ can be produced successfully. Preliminary measurements show that the corrosion resistance of stainless steel surfaces increased sharply when implanting CN+ at 30 keV compared to reference samples, which is interesting from an application point of view in which improved corrosion resistance, surface engineering and short processing time of stainless steel is required. The results are also interesting for novel research in carbon-based mesoporous materials for energy storage applications and as electrode materials for electrochemical capacitors, because of their high surface area, electrical conductivity, chemical stability and low cost.

Importance of sampling frequency when collecting diatoms

KAUST Repository

Wu, Naicheng; Faber, Claas; Sun, Xiuming; Qu, Yueming; Wang, Chao; Ivetic, Snjezana; Riis, Tenna; Ulrich, Uta; Fohrer, Nicola

2016-01-01

There has been increasing interest in diatom-based bio-assessment but we still lack a comprehensive understanding of how to capture diatoms’ temporal dynamics with an appropriate sampling frequency (ASF). To cover this research gap, we collected

Short-Lived Electronically-Excited Diatomic Molecules Cooled via Supersonic Expansion from a Plasma Microjet

Science.gov (United States)

Houlahan, Thomas J., Jr.; Su, Rui; Eden, Gary

2014-06-01

Using a pulsed plasma microjet to generate short-lived, electronically-excited diatomic molecules, and subsequently ejecting them into vacuum to cool via supersonic expansion, we are able to monitor the cooling of molecules having radiative lifetimes as low as 16 ns. Specifically, we report on the rotational cooling of He_2 molecules in the d^3Σ_u^+, e^3Π_g, and f^3Σ_u^+ states, which have lifetimes of 25 ns, 67 ns, and 16 ns, respectively. The plasma microjet is driven with a 2.6 kV, 140 ns high-voltage pulse (risetime of 20 ns) which, when combined with a high-speed optical imaging system, allows the nonequilibrium rotational distribution for these molecular states to be monitored as they cool from 1200 K to below 250 K with spatial and temporal resolutions of below 10 μm and 10 ns, respectively. The spatial and temporal resolution afforded by this system also allows the observation of excitation transfer between the f^3Σ_u^+ state and the lower lying d^3Σ_u^+ and e^3Π_g states. The extension of this method to other electronically excited diatomics with excitation energies >5 eV will also be discussed.

Next Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer Tissue Specimens for Enhanced Clinical Guidance

Science.gov (United States)

2016-07-01

AWARD NUMBER: W81XWH- 14-1-0192 TITLE: Next-Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer...DATES COVERED 4. TITLE AND SUBTITLE Next-Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer Tissue

Biological monitoring of lotic ecosystems: the role of diatoms

Directory of Open Access Journals (Sweden)

T. Bere

Full Text Available Increasing anthropogenic influence on lotic environments as a result of civilisation has captured public interest because of the consequent problems associated with deterioration of water quality. Various biological monitoring methods that provide a direct measure of ecological integrity by using the response of biota to environmental changes have been developed to monitor the ecological status of lotic environments. Diatoms have been used extensively in this regard and this review attempts to summarise the basic concepts associated with biological monitoring using benthic diatoms. Where possible, examples from work carried out in Brazil are used.

Ionic fragmentation channels in electron collisions of small molecular ions

International Nuclear Information System (INIS)

Hoffmann, Jens

2009-01-01

Dissociative Recombination (DR) is one of the most important loss processes of molecular ions in the interstellar medium (IM). Ion storage rings allow to investigate these processes under realistic conditions. At the Heidelberg test storage ring TSR a new detector system was installed within the present work in order to study the DR sub-process of ion pair formation (IPF). The new detector expands the existing electron target setup by the possibility to measure strongly deflected negative ionic fragments. At the TSR such measurements can be performed with a uniquely high energy resolution by independently merging two electron beams with the ion beam. In this work IPF of HD + , H 3 + and HF + has been studied. In the case of HD + the result of the high resolution experiment shows quantum interferences. Analysis of the quantum oscillations leads to a new understanding of the reaction dynamics. For H 3 + it was for the first time possible to distinguish different IPF channels and to detect quantum interferences in the data. Finally the IPF of HF + was investigated in an energy range, where in previous experiments no conclusive results could be obtained. (orig.)

A Rapid Method for the Determination of Fucoxanthin in Diatom

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Li-Juan Wang

2018-01-01

Full Text Available Fucoxanthin is a natural pigment found in microalgae, especially diatoms and Chrysophyta. Recently, it has been shown to have anti-inflammatory, anti-tumor, and anti-obesityactivity in humans. Phaeodactylum tricornutum is a diatom with high economic potential due to its high content of fucoxanthin and eicosapentaenoic acid. In order to improve fucoxanthin production, physical and chemical mutagenesis could be applied to generate mutants. An accurate and rapid method to assess the fucoxanthin content is a prerequisite for a high-throughput screen of mutants. In this work, the content of fucoxanthin in P. tricornutum was determined using spectrophotometry instead of high performance liquid chromatography (HPLC. This spectrophotometric method is easier and faster than liquid chromatography and the standard error was less than 5% when compared to the HPLC results. Also, this method can be applied to other diatoms, with standard errors of 3–14.6%. It provides a high throughput screening method for microalgae strains producing fucoxanthin.

Adaptive significance of phytoplankton stickiness with emphasis on the diatom Skeletonema costatum

DEFF Research Database (Denmark)

Hansen, J.L.S.; Timm, U.; Kiørboe, Thomas

1995-01-01

Diatom aggregate formation was analyzed using coagulation theory. Population dynamics models show that coagulation has an important impact on species succession during diatom blooms. When different species collide and form mixed aggregates this process causes interspecific interference competitio...... was tested on field data, and the predicted dynamics of a spring bloom was very similar to that observed...

Paleoceanographic, and paleoclimatic constraints on the global Eocene diatom and silicoflagellate record

Science.gov (United States)

Barron, John A.; Stickley, Catherine E.; Bukry, David

2015-01-01

Eocene diatom and silicoflagellate biostratigraphy are summarized and correlated with the most recent geologic time scale as well as with the global oxygen isotope and eustatic sea level curves. The global distribution of Eocene diatom/silicoflagellate-bearing sediments varies considerably, reflecting changing oceanic gateways and paleoceanography with changing patterns that are punctuated by four major depositional events.

Diatoms as water quality indicators in the upper reaches of the Great ...

African Journals Online (AJOL)