Indirect mechanisms in electron-impact ionization of multiply charged ions

International Nuclear Information System (INIS)

Phaneuf, R.A.; Gregory, D.C.

1986-09-01

The important role of indirect-ionization mechanisms in electron-impact ionization of multiply charged ions has been emphasized by some recent experiments conducted with the ORNL-ECR multicharged ion source. Illustrative examples of investigations of the Mg-isoelectronic and Fe-isonuclear sequences are presented and compared with the results of detailed theoretical calculations. New experimental data is also presented concerning the role of resonance effects in the ionization of Li-like O 5+ and Na-like Fe 15+ ions

Carbon dynamics in corn-soybean sequences as estimated from natural carbon-13 abundance

International Nuclear Information System (INIS)

Huggins, D.R.; Clapp, C.E.; Allmaras, R.R.; Lamb, J.A.; Layese, M.F.

1998-01-01

Carbon flow in terrestrial ecosystems regulates partitioning between soil organic C (SOC) and atmospheric CO2. Our objectives were to assess SOC dynamics using natural 13C abundance in corn (Zea mays L., a C4 species)-soybean [Glycine max (L.) Merr., a C3 species] sequences. Fifteen treatments of continuous corn, continuous soybean, various sequences of corn and soybean, and fallow were initiated in 1981 at Lamberton, MN, on a Webster clay loam (fine-loamy, mixed, mesic Typic Haplaquoll). In 1991, soil and aboveground shoot samples from all treatments were analyzed for total organic C and delta 13C. Carbon inputs, delta 13C, and SOC were integrated into a two-pool model to evaluate C dynamics of corn and soybean. Total SOC was similar across all treatments after 10 yr; however, differences in soil delta 13C occurred between continuous corn (delta 13C = -17.2 per thous and) and continuous soybean (delta 13C = -18.2 per thousand). Modeled C dynamics showed SOC decay rates of 0.011 yr-1 for C4-derived C and 0.007 yr-1 for C3-derived C, and humification rates of 0.16 yr-1 for corn and 0.11 yr-1 for soybean. Decay and humification rates were slightly lower than those found in other Corn Belt studies. Levels of SOC were predicted to decline an additional 7 to 18% with current C inputs from either corn or soybean, respectively. Annual C additions required for SOC maintenance averaged 5.6 Mg C ha-1, 1.4 to 2.1 times greater than previously reported estimates. Controlled variation in natural 13C abundance in corn-soybean rotations during a 10-yr period adequately traced C dynamics

Metre-scale cyclicity in Middle Eocene platform carbonates in northern Egypt: Implications for facies development and sequence stratigraphy

Science.gov (United States)

Tawfik, Mohamed; El-Sorogy, Abdelbaset; Moussa, Mahmoud

2016-07-01

The shallow-water carbonates of the Middle Eocene in northern Egypt represent a Tethyan reef-rimmed carbonate platform with bedded inner-platform facies. Based on extensive micro- and biofacies documentation, five lithofacies associations were defined and their respective depositional environments were interpreted. Investigated sections were subdivided into three third-order sequences, named S1, S2 and S3. Sequence S1 is interpreted to correspond to the Lutetian, S2 corresponds to the Late Lutetian and Early Bartonian, and S3 represents the Late Bartonian. Each of the three sequences was further subdivided into fourth-order cycle sets and fifth-order cycles. The complete hierarchy of cycles can be correlated along 190 km across the study area, and highlighting a general "layer-cake" stratigraphic architecture. The documentation of the studied outcrops may contribute to the better regional understanding of the Middle Eocene formations in northern Egypt and to Tethyan pericratonic carbonate models in general.

Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks

OpenAIRE

Kumar, Manish; Gazara, Rajesh Kumar; Verma, Sandhya; Kumar, Madan; Verma, Praveen Kumar; Thakur, Indu Shekhar

2016-01-01

The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO2)-sequestering bacterium isolated from marble mining rocks in the Umra area, Rajasthan, India. This strain grows chemolithotrophically on media that contain sodium bicarbonate (NaHCO3) as the sole carbon source. Here, we report the genome sequence of 5.07?Mb Serratia sp. ISTD04.

Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks.

Science.gov (United States)

Kumar, Manish; Gazara, Rajesh Kumar; Verma, Sandhya; Kumar, Madan; Verma, Praveen Kumar; Thakur, Indu Shekhar

2016-10-20

The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO 2 )-sequestering bacterium isolated from marble mining rocks in the Umra area, Rajasthan, India. This strain grows chemolithotrophically on media that contain sodium bicarbonate (NaHCO 3 ) as the sole carbon source. Here, we report the genome sequence of 5.07 Mb Serratia sp. ISTD04. Copyright © 2016 Kumar et al.

Sequence Dependent Interactions Between DNA and Single-Walled Carbon Nanotubes

Science.gov (United States)

Roxbury, Daniel

It is known that single-stranded DNA adopts a helical wrap around a single-walled carbon nanotube (SWCNT), forming a water-dispersible hybrid molecule. The ability to sort mixtures of SWCNTs based on chirality (electronic species) has recently been demonstrated using special short DNA sequences that recognize certain matching SWCNTs of specific chirality. This thesis investigates the intricacies of DNA-SWCNT sequence-specific interactions through both experimental and molecular simulation studies. The DNA-SWCNT binding strengths were experimentally quantified by studying the kinetics of DNA replacement by a surfactant on the surface of particular SWCNTs. Recognition ability was found to correlate strongly with measured binding strength, e.g. DNA sequence (TAT)4 was found to bind 20 times stronger to the (6,5)-SWCNT than sequence (TAT)4T. Next, using replica exchange molecular dynamics (REMD) simulations, equilibrium structures formed by (a) single-strands and (b) multiple-strands of 12-mer oligonucleotides adsorbed on various SWCNTs were explored. A number of structural motifs were discovered in which the DNA strand wraps around the SWCNT and 'stitches' to itself via hydrogen bonding. Great variability among equilibrium structures was observed and shown to be directly influenced by DNA sequence and SWCNT type. For example, the (6,5)-SWCNT DNA recognition sequence, (TAT)4, was found to wrap in a tight single-stranded right-handed helical conformation. In contrast, DNA sequence T12 forms a beta-barrel left-handed structure on the same SWCNT. These are the first theoretical indications that DNA-based SWCNT selectivity can arise on a molecular level. In a biomedical collaboration with the Mayo Clinic, pathways for DNA-SWCNT internalization into healthy human endothelial cells were explored. Through absorbance spectroscopy, TEM imaging, and confocal fluorescence microscopy, we showed that intracellular concentrations of SWCNTs far exceeded those of the incubation

Recognition of depositional sequences and stacking patterns, Late Devonian (Frasnian) carbonate platforms, Alberta basin

Energy Technology Data Exchange (ETDEWEB)

Anderson, J.H.; Reeckmann, S.A.; Sarg, J.F.; Greenlee, S.M.

1987-05-01

Six depositional sequences bounded by regional unconformities or their correlative equivalents (sequence boundaries) have been recognized in Late Devonian (Frasnian) carbonate platforms in the Alberta basin. These sequences consist of a predictable vertical succession of smaller scale shoaling-upward cycles (parasequences). Parasequences are arranged in retrogradational, aggradational, and progradational stacking patterns that can be modeled as a sediment response to relative changes in sea level. Sequence boundaries are recognized by onlap onto underlying shelf or shelf margin strata. This onlap includes shelf margin wedges and deep marine onlap. In outcrop sections shelf margin wedges exhibit an abrupt juxtaposition of shallow water facies over deeper water deposits with no gradational facies changes at the boundaries. High on the platform, subaerial exposure fabrics may be present. The shelf margin wedges are interpreted to have formed during lowstands in sea level and typically exhibit an aggradational stacking pattern. On the platform, two types of sequences are recognized. A type 1 cycle occurs where the sequence boundary is overlain by a flooding surface and subsequent parasequences exhibit retrogradational stacking. In a type 2 cycle the sequence boundary is overlain by an aggradational package of shallow water parasequences, followed by a retrogradational package. These two types of sequences can be modeled using a sinusoidal eustatic sea level curve superimposed on thermo-tectonic subsidence.

Cyclic architecture of a carbonate sequence, early Aptian Shuaiba formation, Al Huwaisah field, Oman

Energy Technology Data Exchange (ETDEWEB)

Groetsch, J. (Shell Research, Rijswijk (Netherlands))

1993-09-01

Sequence stratigraphy of carbonates is a topic of ongoing controversy. In particular, small-scale shallowing-upward cycles can provide some key information needed for interpretation of carbonate sequences and/or third-order sea level changes. The early Aptian Shuaiba Formation in the Al Huwaisah field consists of about 90 m of shallow-water limestones. Throughout the formation, an overall decreasing influx of fine detritus is notable toward the top. The sequence can be subdivided into a basal unit and an overlying unit. Both units are composed of meter-scale shallowing-upward cycles of different composition, which can be recognized in core and well logs. Fourier analysis of the first principle component of a set of well logs (GR, FDC, CNL, Sonic) revealed an abrupt change in spectral behavior between the two units. Toward the top, the spectra are [open quotes]cleaning upward[close quotes] with an increasing pronunciation of a peak grouping of 1: 2: 5, suggesting a better preservation of orbital variations in the upper unit. Preservation of orbital forcing in shallowing-upward cycles requires rapid rates of sedimentation. In addition, increased shallow-water carbonate production on the platform is indicated by the appearance of reefal organisms. Hence, a higher rate of sedimentation and therefore a faster aggradation of the platform is inferred for the upper unit, which could have resulted from an increased rate of relative sea level rise. The sudden facies differentiation on the broad Arabian shelf in the upper part of the early Aptian reflects the development of an intrashelf basin. Changes in rate of relative sea level rise on the Arabian shelf might explain the repeated alternation from an easily correlatable ramp-type sedimentation, with slightly higher input of fine terrigenous sediment (e.g., lower unit of Shuaiba Formation) and a differentiation into platform and intrashelf basin facies due to faster aggradation (e.g., upper unit of Shuaiba Formation).

Distorted-wave calculations of electron impact ionisation in the Ni isonuclear sequence

Energy Technology Data Exchange (ETDEWEB)

Griffin, D C; Pindzola, M S

1988-10-14

Electron impact ionisation cross sections for Ni/sup +/, Ni/sup 3+/, Ni/sup 5+/, Ni/sup 6+/, Ni/sup 7+/, Ni/sup 8+/, Ni/sup 12+/, Ni/sup 14+/, and Ni/sup 16+/ are calculated in the distorted-wave approximation. These calculations include contributions from direct ionisation and inner-shell excitation followed by autoionisation. For Ni/sup 12+/, Ni/sup 14+/, and Ni/sup 16+/ we report not only on ionisation cross sections from the ground states but also from the metastable states of these ions. Experimental cross section measurements exist for all ions reported here, except Ni/sup 16+/. The agreement between experiment and theory is reasonably good and improves with ionisation stage.

The effect of the multi-pass non-circular drawing sequence on mechanical properties and microstructure evolution of low-carbon steel

International Nuclear Information System (INIS)

Lee, Jung Wan; Baek, Hyun Moo; Hwang, Sun Kwang; Son, Il-Heon; Bae, Chul Min; Im, Yong-Taek

2014-01-01

Highlights: • A multi-pass non-circular drawing sequence is proposed to make high-strength wires. • The sequence was designed and applied for a low-carbon steel wire up to the 10th pass. • Many LAGBs and small grain size of the wire produced by the sequence were obtained. • High plastic deformation was imposed on the wire, resulting in grain refinement. • The sequence made fine-grained wires with improved UTS, ductility and fatigue life. - Abstract: In this study, the multi-pass non-circular drawing sequence was investigated for manufacturing high-strength wires with better ductility in a simple continuous way without adding additional alloys and heat treatment considering the effect of microstructure evolution and die geometry of the sequence on the mechanical properties of low-carbon steel during the process. For this purpose, the non-circular drawing sequence was designed and applied up to the 10th pass at room temperature. Mechanical properties and microstructure evolution of the specimen processed by the sequence were investigated by tension, Vickers micro-hardness, electron backscattering diffraction (EBSD), and fatigue tests compared with those for the conventional wire-drawing process. From the EBSD results, the higher low angle grain boundaries length per unit area and smaller average grain size of the specimen processed by the non-circular drawing sequence were obtained than those of the specimen processed by the wire-drawing process for the 8th pass. These results indicated that more plastic deformation was imposed in the material by the non-circular drawing sequence, resulting in grain refinement of the deformed specimen compared to the wire-drawing process. It is demonstrated that the multi-pass non-circular drawing sequence could be beneficial in producing fine-grained wires with improved ultimate tensile strength, ductility, and fatigue property by simply changing drawing dies geometry of the conventional wire-drawing process

Effects of stacking sequence on fracture mechanisms in quasi-isotropic Carbon/epoxy laminates under tensile loading

International Nuclear Information System (INIS)

Hessabi, Z. R.; Majidi, B.; Aghazadeh, J.

2006-01-01

The progress of damage in quasi-isotropic carbon/epoxy laminates under tensile loading has been Investigated microscopically. One significant mode of failure in laminated composites is delamination initiating at free edges. The interlaminar stress in the boundary ply along the free edges of a laminated composite is the main factor to cause delamination. The laminate stacking sequence affects the interlaminar stress distribution and consequently may change the mode of failure. It is of design importance to determine a suitable criterion based on stress analysis to obtain the best stacking sequence. In the present work, tensile properties of six samples with different stacking sequences have been examined. Results showed that stress analysis at distance very close to the free edges is a suitable criterion to predict the initiation of delamination and the stacking sequence of [90/45/0/-45] s , has the highest strength among the others. Furthermore finite element analysis showed that the adjacent ±45 plies cause premature delamination during tensile loading

The sequence stratigraphy, sedimentology, and economic importance of evaporite carbonate transitions: a review

Science.gov (United States)

Sarg, J. F.

2001-04-01

World-class hydrocarbon accumulations occur in many ancient evaporite-related basins. Seals and traps of such accumulations are, in many cases, controlled by the stratigraphic distribution of carbonate-evaporite facies transitions. Evaporites may occur in each of the systems tracts within depositional sequences. Thick evaporite successions are best developed during sea level lowstands due to evaporative drawdown. Type 1 lowstand evaporite systems are characterized by thick wedges that fill basin centers, and onlap basin margins. Very thick successions (i.e. saline giants) represent 2nd-order supersequence set (20-50 m.y.) lowstand systems that cap basin fills, and provide the ultimate top seals for the hydrocarbons contained within such basins. Where slope carbonate buildups occur, lowstand evaporites that onlap and overlap these buildups show a lateral facies mosaic directly related to the paleo-relief of the buildups. This facies mosaic, as exemplified in the Silurian of the Michigan basin, ranges from nodular mosaic anhydrite of supratidal sabkha origin deposited over the crests of the buildups, to downslope subaqueous facies of bedded massive/mosaic anhydrite and allochthonous dolomite-anhydrite breccias. Facies transitions near the updip onlap edges of evaporite wedges can provide lateral seals to hydrocarbons. Porous dolomites at the updip edges of lowstand evaporites will trap hydrocarbons where they onlap nonporous platform slope deposits. The Desert Creek Member of the Paradox Formation illustrates this transition. On the margins of the giant Aneth oil field in southeastern Utah, separate downdip oil pools have accumulated where dolomudstones and dolowackestones with microcrystalline porosity onlap the underlying highstand platform slope. Where lowstand carbonate units exist in arid basins, the updip facies change from carbonates to evaporite-rich facies can also provide traps for hydrocarbons. The change from porous dolomites composed of high

Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901.

Science.gov (United States)

Wu, Martin; Ren, Qinghu; Durkin, A Scott; Daugherty, Sean C; Brinkac, Lauren M; Dodson, Robert J; Madupu, Ramana; Sullivan, Steven A; Kolonay, James F; Haft, Daniel H; Nelson, William C; Tallon, Luke J; Jones, Kristine M; Ulrich, Luke E; Gonzalez, Juan M; Zhulin, Igor B; Robb, Frank T; Eisen, Jonathan A

2005-11-01

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a "minimal" model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously.

Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901.

Directory of Open Access Journals (Sweden)

2005-11-01

Full Text Available We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a "minimal" model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously.

Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901.

Directory of Open Access Journals (Sweden)

Martin Wu

2005-11-01

Full Text Available We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a "minimal" model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously.

Effects of heavy metals and phenol on the operation of sequencing batch reactor added activated carbon

Energy Technology Data Exchange (ETDEWEB)

Lee, Sang Hoon; Lim, Ji Hun; Park, Chul Hwan; Lee, Jin Won [Dept. of Chemical Engineering, Kwangwoon University, Seoul (Korea); Kim, Sang Yong [Korea Institute of Industrial Technology (Korea); Park, Jin Yong [Dept. of Environmental Engineering, Hallym University (Korea); Lee, Yong Myun [Osung Envi-Tech Company (Korea)

2000-04-01

The process of sequencing batch reactor(SBR) added the activated carbon were studied. To investigate the influence of the activated carbon on the treatment of organic materials and the effects of heavy metals on the process, three different kinds of granular activated carbons(GAC) were tested. Teh decrease of SCOD(soluble chemical oxygen demand) was measured at the different concentrations of the activated carbon. Synergistic effects of GAC on the biological activity in the SBR were confirmed from the data comparing adsorbed loadings with apparent loadings. When SBR was operated with GAC, the efficiency of wastewater treatment increased 16%. By comparing the adsorbed amount of SCOD estimated from Freundlich isotherm and the decrease of apparent loading, biological synergistic effect was confirmed. The inhibition of SBR performance from heavy metals or toxic chemicals could be reduced when GAC was added into the SBR process. Pb, Cd, Cr, and phenol were tested as typical inhibitors. When 10mg/L inhibitor was introduced into the SBR process which includes 500 mg/L GAC, the efficiency was increased as 32.6%, 27.2%, 22.3%, and 9.4%, respectively. 22 refs., 13 figs., 3 tabs.

Spectral Sequences of Type Ia Supernovae. I. Connecting Normal and Subluminous SNe Ia and the Presence of Unburned Carbon

Energy Technology Data Exchange (ETDEWEB)

Heringer, E.; Kerkwijk, M. H. van [Department of Astronomy and Astrophysics, University of Toronto, 50 Saint George Street, Toronto, ON M5S 3H4 (Canada); Sim, S. A. [Astrophysics Research Centre, School of Mathematics and Physics, Queens University Belfast, Belfast BT7 1NN (United Kingdom); Kerzendorf, W. E. [European Southern Observatory (ESO), Karl-Schwarzschild-Straße 2, D-85748 Garching (Germany)

2017-09-01

Type Ia supernovae (SNe Ia) are generally agreed to arise from thermonuclear explosions of carbon–oxygen white dwarfs. The actual path to explosion, however, remains elusive, with numerous plausible parent systems and explosion mechanisms suggested. Observationally, SNe Ia have multiple subclasses, distinguished by their light curves and spectra. This raises the question of whether these indicate that multiple mechanisms occur in nature or that explosions have a large but continuous range of physical properties. We revisit the idea that normal and 91bg-like SNe can be understood as part of a spectral sequence in which changes in temperature dominate. Specifically, we find that a single ejecta structure is sufficient to provide reasonable fits of both the normal SN Ia SN 2011fe and the 91bg-like SN 2005bl, provided that the luminosity and thus temperature of the ejecta are adjusted appropriately. This suggests that the outer layers of the ejecta are similar, thus providing some support for a common explosion mechanism. Our spectral sequence also helps to shed light on the conditions under which carbon can be detected in premaximum SN Ia spectra—we find that emission from iron can “fill in” the carbon trough in cool SNe Ia. This may indicate that the outer layers of the ejecta of events in which carbon is detected are relatively metal-poor compared to events in which carbon is not detected.

Sedimentology and High Resolution Sequence Stratigraphy of the Middle Jurassic Dhruma Formation Carbonates Outcrops in the Central Saudi Arabia

Science.gov (United States)

Yousif, Ibrahim; Abdullatif, Osman; Makkawi, Mohammed; Abdulghani, Waleed

2017-04-01

This study investigates the microfacies and sequence stratigraphic frame work of the Middle Jurassic Dhruma Formation in outcrops in central Saudi Arabia. The study contributes to the efforts to understand and enhance local and regional stratigraphic relationship and correlation of the Jurassic carbonate sequences and their significance to reservoir description and prediction in the subsurcae. The study describes and characterizes the sedimentology, microfacies and the stratigraphy of Dhruma Formation from outcrop sections having a total thickness of 70 m. Detailed microfacies and high-resolution stratigraphical analysis were carried out to determine microfacies, cyclicity, sequences and staking pattern. The study revealed ten lithofacies namely: oolitic grainstone,bioclastic oolitic grainstone, oolitic grapestone, bioclastic grainstone,foraminiferal packstone, echinoderm packstone, peloidal packstone to grainstone,skeletal wackestone to packstone, mudstone, and marlstone.These lithofacies were grouped into five lithofacies associations that deposited on a carbonate ramp setting. The depositional environment ranging from low energy lagoonal setting to high-energy shoals and banks to low energy outer ramp setting. Five high-resolution composite sequences have been defined and each sequence is composed at the bottom of intercalated mudstone/wackestone that passing up into grainstone lithofacies.The composite sequences range in thickness from 7 to 15 m, while the parasequences range from 0.5 to 1.5 m. The composite sequences extend laterally for a distance of more than 350 m. The overall composite section shows a shallowing upward succession of the 4th to the 5th order high-resolution sequences.The dominant lithofacies are the grainy ones, which constitute 30%, 50% and 80% of the studied sections. Furthermore, the parasequences thickness and their bio-components are increasing towards the top. The muddy lithofacies intensively affected the vertical continuity of the

Integrated analysis of 454 and Illumina transcriptomic sequencing characterizes carbon flux and energy source for fatty acid synthesis in developing Lindera glauca fruits for woody biodiesel.

Science.gov (United States)

Lin, Zixin; An, Jiyong; Wang, Jia; Niu, Jun; Ma, Chao; Wang, Libing; Yuan, Guanshen; Shi, Lingling; Liu, Lili; Zhang, Jinsong; Zhang, Zhixiang; Qi, Ji; Lin, Shanzhi

2017-01-01

Lindera glauca fruit with high quality and quantity of oil has emerged as a novel potential source of biodiesel in China, but the molecular regulatory mechanism of carbon flux and energy source for oil biosynthesis in developing fruits is still unknown. To better develop fruit oils of L. glauca as woody biodiesel, a combination of two different sequencing platforms (454 and Illumina) and qRT-PCR analysis was used to define a minimal reference transcriptome of developing L. glauca fruits, and to construct carbon and energy metabolic model for regulation of carbon partitioning and energy supply for FA biosynthesis and oil accumulation. We first analyzed the dynamic patterns of growth tendency, oil content, FA compositions, biodiesel properties, and the contents of ATP and pyridine nucleotide of L. glauca fruits from seven different developing stages. Comprehensive characterization of transcriptome of the developing L. glauca fruit was performed using a combination of two different next-generation sequencing platforms, of which three representative fruit samples (50, 125, and 150 DAF) and one mixed sample from seven developing stages were selected for Illumina and 454 sequencing, respectively. The unigenes separately obtained from long and short reads (201, and 259, respectively, in total) were reconciled using TGICL software, resulting in a total of 60,031 unigenes (mean length = 1061.95 bp) to describe a transcriptome for developing L. glauca fruits. Notably, 198 genes were annotated for photosynthesis, sucrose cleavage, carbon allocation, metabolite transport, acetyl-CoA formation, oil synthesis, and energy metabolism, among which some specific transporters, transcription factors, and enzymes were identified to be implicated in carbon partitioning and energy source for oil synthesis by an integrated analysis of transcriptomic sequencing and qRT-PCR. Importantly, the carbon and energy metabolic model was well established for oil biosynthesis of developing L

Carbonate deposition, Pyramid Lake subbasin, Nevada: 1. Sequence of formation and elevational distribution of carbonate deposits (Tufas)

Science.gov (United States)

Benson, L.

1994-01-01

During the late Quarternary, the elevation of terrace cutting and carbonate deposition in the Pyramid Lake subbasin were controlled by constancy of lake level imposed by spill to adjoining subbasins. Sill elevations are 1177-1183 m (Mud Lake Slough Sill), 1207 m (Emerson Pass Sill), and 1265 m (Darwin Pass Sill). Carbonate deposition was favored by: (1) hydrologic closure, (2) proximity to a source of calcium, (3) elevated water temperature, and (4) a solid substrate. The thickness and aspect of tufa are a function oflake-level dynamics. Relatively thin sheets and pendant sheets were deposited during a rising or falling lake. The upper parts of thick reef-form tufas have a horizontal aspect and were deposited in a lake which was stabilized by spill to the Carson Desert subbasin. The lower parts of the reef-form tufas are thinner and their outer surface has a vertical aspect, indicating that the lower part formed in a receding lake. The thickest and most complete sequences of tufa are mounds that border the Pyramid Lake shore. The tops of the tallest mounds reach the elevation of the Darwin Pass Sill and many mounds have been eroded to the elevations of the Mud Lake Slough Sill of the Emerson Pass Sill. The sequence of tufa formation (from oldest to youngest) displayed in these mounds is: (1) a beachrock containing carbonate-cemented volcanic cobbles, (2) broken and eroded old spheroids that contain thinolitic tufa and an outer rind of dense laminated tufa, (3) large cylindrical (tubular) tufas capped by (4) coatings of old dense tufas, and (5) several generations of old branching tufa commonly associated with thin, platy tufas and coatings of thinolitic tufa, (6) young spheroids that contain poorly oriented young thinolitic tufa in the center and several generations of radially oriented young thinolitic tufas near the outer edge, (7) a transitional thinolite-to-branching tufa, (8) two or more layers of young branching tufa, (9) a 0.5-cm-thick layer of fine

Atomic Decay Data for Modeling K Lines of Iron Peak and Light Odd-Z Elements*

Science.gov (United States)

Palmeri, P.; Quinet, P.; Mendoza, C.; Bautista, M. A.; Garcia, J.; Witthoeft, M. C.; Kallman, T. R.

2012-01-01

Complete data sets of level energies, transition wavelengths, A-values, radiative and Auger widths and fluorescence yields for K-vacancy levels of the F, Na, P, Cl, K, Sc, Ti, V, Cr, Mn, Co, Cu and Zn isonuclear sequences have been computed by a Hartree-Fock method that includes relativistic corrections as implemented in Cowan's atomic structure computer suite. The atomic parameters for more than 3 million fine-structure K lines have been determined. Ions with electron number N greater than 9 are treated for the first time, and detailed comparisons with available measurements and theoretical data for ions with N less than or equal to 9 are carried out in order to estimate reliable accuracy ratings.

Minimizing N2O emissions and carbon footprint on a full-scale activated sludge sequencing batch reactor.

Science.gov (United States)

Rodriguez-Caballero, A; Aymerich, I; Marques, Ricardo; Poch, M; Pijuan, M

2015-03-15

A continuous, on-line quantification of the nitrous oxide (N2O) emissions from a full-scale sequencing batch reactor (SBR) placed in a municipal wastewater treatment plant (WWTP) was performed in this study. In general, N2O emissions from the biological wastewater treatment system were 97.1 ± 6.9 g N2O-N/Kg [Formula: see text] consumed or 6.8% of the influent [Formula: see text] load. In the WWTP of this study, N2O emissions accounted for over 60% of the total carbon footprint of the facility, on average. Different cycle configurations were implemented in the SBR aiming at reaching acceptable effluent values. Each cycle configuration consisted of sequences of aerated and non-aerated phases of different time length being controlled by the ammonium set-point fixed. Cycles with long aerated phases showed the largest N2O emissions, with the consequent increase in carbon footprint. Cycle configurations with intermittent aeration (aerated phases up to 20-30 min followed by short anoxic phases) were proven to effectively reduce N2O emissions, without compromising nitrification performance or increasing electricity consumption. This is the first study in which a successful operational strategy for N2O mitigation is identified at full-scale. Copyright © 2014 Elsevier Ltd. All rights reserved.

Carbon Isotope Chemostratigraphy, the Baby and the Bathwater

Science.gov (United States)

Arthur, M. A.

2008-12-01

Secular variations in the carbon isotopic values of carbonate sediments and rocks and their individual components have been applied successfully to problems of stratigraphic correlation and for interpretation of past changes in the global carbon cycle. However, this methodology is not without problems. A major tenet of stable isotope chemostratigraphy involves sampling and analyzing multiple, widely separated sequences, and, if possible, multiple carbon-bearing components (e.g., carbonate and organic carbon) in order to demonstrate a global signal. In some cases, this methodology has been short-circuited in the zeal to reveal a new event or excursion, particularly for time intervals for which adequate sequences are somewhat rare. Likewise, although most carbonate researchers are quite aware of the possible importance of diagenesis, particularly in organic-carbon rich sequences or in shoal-water carbonate sequences with longer-term subaerial exposure events, such overprints commonly go unrecognized or are considered of minor impact. Studies of stable isotope variations in carbonate sequences should always employ textural and geochemical methodologies for detecting and even quantifying diagenesis, if possible. Although some diagenetically overprinted or misinterpreted geochemical data have undoubtedly appeared in the literature, there are many excellent examples of global carbon isotope variations in records expressed in pelagic biogenic carbonate, marine organic carbon, platform carbonates, and terrestrial organic matter. Arguably, one of the best-documented examples is the Cenomanian-Turonian (ca. 93 Ma) positive carbon isotope excursion. The amplitude of the Cenomanian-Turonian carbon isotope excursion is similar among all types of records, but there are subtle pattern differences that arise from differences in sedimentation rate among and within sequences. Organic carbon and carbonate carbon isotope signals also may differ in phasing and amplitude for certain

Stratigraphical analysis of the neoproterozoic sedimentary sequences of the Sao Francisco Basin

International Nuclear Information System (INIS)

Martins, Mariela; Lemos, Valesca Brasil

2007-01-01

A stratigraphic analysis was performed under the principles of Sequence Stratigraphy on the neoproterozoic sedimentary sequences of the Sao Francisco Basin (Central Brazil). Three periods of deposition separated by unconformities were recognized in the Sao Francisco Megasequence: (1) Sequences 1 and 2, a cryogenian glaciogenic sequence, followed by a distal scarp carbonate ramp, developed during stable conditions, (2) Sequence 3, a Upper Cryogenian stack homoclinal ramps with mixed carbonate-siliciclastic sedimentation, deposited under a progressive influence of compressional stresses of the Brasiliano Cycle, (3) Sequence 4, a Lower Ediacaran shallow platform dominated by siliciclastic sedimentation of molassic nature, the erosion product of the nearby uplifted thrust sheets. Each of the carbonate-bearing sequences presents a distinct δ 13 C isotopic signature. The superposition to the global curve for carbon isotopic variation allowed the recognition of a major depositional hiatus between the Paranoa and Sao Francisco Megasequences, and suggested that the glacial diamictite deposition (Jequitai Formation) took place most probably around 800 Ma. This constrains the Sao Francisco Megasequence deposition to the interval between 800 and 600 Ma (the known ages of the Brasiliano Orogeny defines the upper limit). A minor depositional hiatus (700.680 Ma) was also identified separating sequences 2 and 3. Isotopic analyses suggest that from then on, more restricted environmental conditions were established in the basin, probably associated with a first order global event, which prevailed throughout deposition of the Sequence 3. (author)

Controls on facies and sequence stratigraphy of an upper Miocene carbonate ramp and platform, Melilla basin, NE Morocco

Science.gov (United States)

Cunningham, K.J.; Collins, Luke S.

2002-01-01

Upwelling of cool seawater, paleoceanographic circulation, paleoclimate, local tectonics and relative sea-level change controlled the lithofacies and sequence stratigraphy of a carbonate ramp and overlying platform that are part of a temporally well constrained carbonate complex in the Melilla basin, northeastern Morocco. At Melilla, from oldest to youngest, a third-order depositional sequence within the carbonate complex contains (1) a retrogradational, transgressive, warm temperate-type rhodalgal ramp; (2) an early highstand, progradational, bioclastic platform composed mainly of a temperate-type, bivalve-rich molechfor facies; and (3) late highstand, progradational to downstepping, subtropical/tropical-type chlorozoan fringing Porites reefs. The change from rhodalgal ramp to molechfor platform occurred at 7.0??0.14 Ma near the Tortonian/Messinian boundary. During a late stage in the development of the bioclastic platform a transition from temperate-type molechfor facies to subtropical/tropical-type chlorozoan facies occurred and is bracketed by chron 3An.2n (??? 6.3-6.6 Ma). Comparison to a well-dated carbonate complex in southeastern Spain at Cabo de Gata suggests that upwelling of cool seawater influenced production of temperate-type limestone within the ramp and platform at Melilla during postulated late Tortonian-early Messinian subtropical/tropical paleoclimatic conditions in the western Paleo-Mediterranean region. The upwelling of cool seawater across the bioclastic platform at Melilla could be related to the beginning of 'siphoning' of deep, cold Atlantic waters into the Paleo-Mediterranean Sea at 7.17 Ma. The facies change within the bioclastic platform from molechfor to chlorozoan facies may be coincident with a reduction of the siphoning of Atlantic waters and the end of upwelling at Melilla during chron 3An.2n. The ramp contains one retrogradational parasequence and the bioclastic platform three progradational parasequences. Minor erosional surfaces

Constraining controls on carbonate sequences with high-resolution chronostratigraphy: Upper Miocene, Cabo de Gata region, SE Spain

Science.gov (United States)

Montgomery, P.; Farr, M.R.; Franseen, E.K.; Goldstein, R.H.

2001-01-01

A high-resolution chronostratigraphy has been developed for Miocene shallow-water carbonate strata in the Cabo de Gata region of SE Spain for evaluation of local, regional and global factors that controlled platform architecture prior to and during the Messinian salinity crisis. Paleomagnetic data were collected from strata at three localities. Mean natural remanent magnetization (NRM) ranges between 1.53 ?? 10-8 and 5.2 ?? 10-3 Am2/kg. Incremental thermal and alternating field demagnetization isolated the characteristic remanent magnetization (ChRM). Rock magnetic studies show that the dominant magnetic mineral is magnetite, but mixtures of magnetite and hematite occur. A composite chronostratigraphy was derived from five stratigraphic sections. Regional stratigraphic data, biostratigraphic data, and an 40Ar/39Ar date of 8.5 ?? 0.1 Ma, for an interbedded volcanic flow, place the strata in geomagnetic polarity Chrons C4r to C3r. Sequence-stratigraphic and diagenetic evidence indicate a major unconformity at the base of depositional sequence (DS)3 that contains a prograding reef complex, suggesting that approximately 250 000 yr of record (Subchrons C3Br.2r to 3Br.1r) are missing near the Messinian-Tortonian boundary. Correlation to the GPTS shows that the studied strata represent five third- to fourth-order DSs. Basal units are temperate to subtropical ramps (DS1A, DS1B, DS2); these are overlain by subtropical to tropical reefal platforms (DS3), which are capped by subtropical to tropical cyclic carbonates (Terminal Carbonate Complex, TCC). Correlation of the Cabo de Gata record to the Melilla area of Morocco, and the Sorbas basin of Spain indicate that early - Late Tortonian ramp strata from these areas are partially time-equivalent. Similar strata are extensively developed in the Western Mediterranean and likely were influenced by a cool climate or influx of nutrients during an overall rise in global sea-level. After ramp deposition, a sequence boundary (SB3) in

Quantitative controls on location and architecture of carbonate depositional sequences: upper miocene, cabo de gata region, se Spain

Science.gov (United States)

Franseen, E.K.; Goldstein, R.H.; Farr, M.R.

1998-01-01

Sequence stratigraphy, pinning-point relative sea-level curves, and magnetostratigraphy provide the quantitative data necessary to understand how rates of sea-level change and different substrate paleoslopes are dominant controls on accumulation rate, carbonate depositional sequence location, and internal architecture. Five third-order (1-10 my) and fourth-order (0.1-1.0 my) upper Miocene carbonate depositional sequences (DS1A, DS1B, DS2, DS3, TCC) formed with superimposed higher-frequency sea-level cycles in an archipelago setting in SE Spain. Overall, our study indicates when areas of high substrate slope (> 15??) are in shallow water, independent of climate, the location and internal architecture of carbonate deposits are not directly linked to sea-level position but, instead, are controlled by location of gently sloping substrates and processes of bypass. In contrast, if carbonate sediments are generated where substrates of low slope ( 15.6 cm/ky to ??? 2 cm/ky and overall relative sea level rose at rates of 17-21.4 cm/ky. Higher frequency sea-level rates were about 111 to more than 260 cm/ky, producing onlapping, fining- (deepening-) upward cycles. Decreasing accumulation rates resulted from decreasing surface area for shallow-water sediment production, drowning of shallow-water substrates, and complex sediment dispersal related to the archipelago setting. Typical systems tract and parasequence development should not be expected in "bypass ramp" settings; facies of onlapping strata do not track base level and are likely to be significantly different compared to onlapping strata associated with coastal onlap. Basal and upper DS2 reef megabreccias (indicating the transition from cool to warmer climatic conditions) were eroded from steep upslope positions and redeposited downslope onto areas of gentle substrate during rapid sea-level falls (> 22.7 cm/ky) of short duration. Such rapid sea-level falls and presence of steep slopes are not conducive to formation of

FACIES PARTITIONING AND SEQUENCE STRATIGRAPHY OF A MIXED SILICICLASTIC-CARBONATE RAMP STACK IN THE GELASIAN OF SICILY (S ITALY: A POTENTIAL MODEL FOR ICEHOUSE, DISTALLY-STEEPENED HETEROZOAN RAMPS

Directory of Open Access Journals (Sweden)

FRANCESCO MASSARI

2012-11-01

Full Text Available The Gelasian succession of the Capodarso area (Enna-Caltanissetta basin, Sicily, Italy consists of an offlapping stack of cycles composed of siliciclastic units passing to carbonate heterozoan, clino-stratified wedges, developed from a growing positive tectonic structure. Identification of a number of facies tracts, based on sedimentary facies, biofacies and taphofacies, provided important information about the differentiation and characterisation of systems tracts and key stratal surfaces of sequence stratigraphy. The bulk of carbonate wedges are interpreted as representing the rapid falling-stage progradation of distally steepened ramps. The inferred highest rate of carbonate production during forced regressions was concomitant with active downramp resedimentation by storm-driven downwelling flows, leading to storing of most carbonate sediment on the ramp slope as clino-beds of the prograding bodies. Comparison of the Capodarso ramps with other icehouse carbonate ramps, with particular regard to the Mediterranean Plio-Pleistocene, provides clues for defining some common features. These are inferred to include: (1 brief, rapid episodes of progradation concomitant with orbitally-forced sea-level changes, resulting in limited ramp width; (2 preferential fostering of growth and downramp resedimentation of heterozoan carbonates during glacial hemicycles marked by enhanced atmospheric and marine circulation; (3 building out from positive features of entirely submerged distally-steepened ramps with storm-wave-graded profile and distinctive clinoforms; (4 ramp stacks generally consisting of mixed clastic-carbonate sequences showing an ordered spectrum of distinct frequencies; (5 rapid, continuous changes in environmental parameters, leading to the short-lived persistence of faunal communities, climax communities generally having insufficient time to form. 

Characteristics, stratigraphic architecture, and time framework of multi-order mixed siliciclastic and carbonate depositional sequences, outcropping Cisco Group (Late Pennsylvanian and Early Permian), Eastern Shelf, north-central Texas, USA

Science.gov (United States)

Yang, Wan; Kominz, Michelle A.

2003-01-01

The Cisco Group on the Eastern Shelf of the Midland Basin is composed of fluvial, deltaic, shelf, shelf-margin, and slope-to-basin carbonate and siliciclastic rocks. Sedimentologic and stratigraphic analyses of 181 meter-to-decimeter-scale depositional sequences exposed in the up-dip shelf indicated that the siliciclastic and carbonate parasequences in the transgressive systems tracts (TST) are thin and upward deepening, whereas those in highstand systems tracts (HST) are thick and upward shallowing. The sequences can be subdivided into five types on the basis of principal lithofacies, and exhibit variable magnitude of facies shift corresponding to variable extents of marine transgression and regression on the shelf. The sequence stacking patterns and their regional persistence suggest a three-level sequence hierarchy controlled by eustasy, whereas local and regional changes in lithology, thickness, and sequence type, magnitude, and absence were controlled by interplay of eustasy, differential shelf subsidence, depositional topography, and pattern of siliciclastic supply. The outcropping Cisco Group is highly incomplete with an estimated 6-11% stratigraphic completeness. The average duration of deposition of the major (third-order) sequences is estimated as 67-102 ka on the up-dip shelf and increases down dip, while the average duration of the major sequence boundaries (SB) is estimated as 831-1066 ka and decreases down dip. The nondepositional and erosional hiatus on the up-dip shelf was represented by lowstand deltaic systems in the basin and slope.

Apoptosis-inducing signal sequence mutation in carbonic anhydrase IV identified in patients with the RP17 form of retinitis pigmentosa

Science.gov (United States)

Rebello, George; Ramesar, Rajkumar; Vorster, Alvera; Roberts, Lisa; Ehrenreich, Liezle; Oppon, Ekow; Gama, Dumisani; Bardien, Soraya; Greenberg, Jacquie; Bonapace, Giuseppe; Waheed, Abdul; Shah, Gul N.; Sly, William S.

2004-01-01

Genetic and physical mapping of the RP17 locus on 17q identified a 3.6-megabase candidate region that includes the gene encoding carbonic anhydrase IV (CA4), a glycosylphosphatidylinositol-anchored protein that is highly expressed in the choriocapillaris of the human eye. By sequencing candidate genes in this region, we identified a mutation that causes replacement of an arginine with a tryptophan (R14W) in the signal sequence of the CA4 gene at position -5 relative to the signal sequence cleavage site. This mutation was found to cosegregate with the disease phenotype in two large families and was not found in 36 unaffected family members or 100 controls. Expression of the mutant cDNA in COS-7 cells produced several findings, suggesting a mechanism by which the mutation can explain the autosomal dominant disease. In transfected COS-7 cells, the R14W mutation (i) reduced the steady-state level of carbonic anhydrase IV activity expressed by 28% due to a combination of decreased synthesis and accelerated turnover; (ii) led to up-regulation of immunoglobulin-binding protein, double-stranded RNA-regulated protein kinase-like ER kinase, and CCAAT/enhancer-binding protein homologous protein, markers of the unfolded protein response and endoplasmic reticulum stress; and (iii) induced apoptosis, as evidenced by annexin V binding and terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling staining, in most cells expressing the mutant, but not the WT, protein. We suggest that a high level of expression of the mutant allele in the endothelial cells of the choriocapillaris leads to apoptosis, leading in turn to ischemia in the overlying retina and producing autosomal dominant retinitis pigmentosa. PMID:15090652

DNA sequencing, anatomy, and calcification patterns support a monophyletic, subarctic, carbonate reef-forming Clathromorphum (Hapalidiaceae, Corallinales, Rhodophyta).

Science.gov (United States)

Adey, Walter H; Hernandez-Kantun, Jazmin J; Johnson, Gabriel; Gabrielson, Paul W

2015-02-01

For the first time, morpho-anatomical characters that were congruent with DNA sequence data were used to characterize several genera in Hapalidiaceae-the major eco-engineers of Subarctic carbonate ecosystems. DNA sequencing of three genes (SSU, rbcL, ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit gene and psbA, photosystem II D1 protein gene), along with patterns of cell division, cell elongation, and calcification supported a monophyletic Clathromorphum. Two characters were diagnostic for this genus: (i) cell division, elongation, and primary calcification occurred only in intercalary meristematic cells and in a narrow vertical band (1-2 μm wide) resulting in a "meristem split" and (ii) a secondary calcification of interfilament crystals was also produced. Neopolyporolithon was resurrected for N. reclinatum, the generitype, and Clathromorphum loculosum was transferred to this genus. Like Clathromorphum, cell division, elongation, and calcification occurred only in intercalary meristematic cells, but in a wider vertical band (over 10-20 μm), and a "meristem split" was absent. Callilithophytum gen. nov. was proposed to accommodate Clathromorphum parcum, the obligate epiphyte of the northeast Pacific endemic geniculate coralline, Calliarthron. Diagnostic for this genus were epithallial cells terminating all cell filaments (no dorsi-ventrality was present), and a distinct "foot" was embedded in the host. Leptophytum, based on its generitype, L. laeve, was shown to be a distinct genus more closely related to Clathromorphum than to Phymatolithon. All names of treated species were applied unequivocally by linking partial rbcL sequences from holotype, isotype, or epitype specimens with field-collected material. Variation in rbcL and psbA sequences suggested that multiple species may be passing under each currently recognized species of Clathromorphum and Neopolyporolithon. © 2014 Phycological Society of America.

Enhanced biological phosphorus removal in a sequencing batch reactor using propionate as the sole carbon source.

Science.gov (United States)

Pijuan, M; Saunders, A M; Guisasola, A; Baeza, J A; Casas, C; Blackall, L L

2004-01-05

An enhanced biological phosphorus removal (EBPR) system was developed in a sequencing batch reactor (SBR) using propionate as the sole carbon source. The microbial community was followed using fluorescence in situ hybridization (FISH) techniques and Candidatus 'Accumulibacter phosphatis' were quantified from the start up of the reactor until steady state. A series of SBR cycle studies was performed when 55% of the SBR biomass was Accumulibacter, a confirmed polyphosphate accumulating organism (PAO) and when Candidatus 'Competibacter phosphatis', a confirmed glycogen-accumulating organism (GAO), was essentially undetectable. These experiments evaluated two different carbon sources (propionate and acetate), and in every case, two different P-release rates were detected. The highest rate took place while there was volatile fatty acid (VFA) in the mixed liquor, and after the VFA was depleted a second P-release rate was observed. This second rate was very similar to the one detected in experiments performed without added VFA.A kinetic and stoichiometric model developed as a modification of Activated Sludge Model 2 (ASM2) including glycogen economy, was fitted to the experimental profiles. The validation and calibration of this model was carried out with the cycle study experiments performed using both VFAs. The effect of pH from 6.5 to 8.0 on anaerobic P-release and VFA-uptake and aerobic P-uptake was also studied using propionate. The optimal overall working pH was around 7.5. This is the first study of the microbial community involved in EBPR developed with propionate as a sole carbon source along with detailed process performance investigations of the propionate-utilizing PAOs. Copyright 2003 Wiley Periodicals, Inc.

X-RAY REFLECTED SPECTRA FROM ACCRETION DISK MODELS. I. CONSTANT DENSITY ATMOSPHERES

International Nuclear Information System (INIS)

Garcia, J.; Kallman, T. R.

2010-01-01

We present new models for illuminated accretion disks, their structure, and reprocessed emission. We consider the effects of incident X-rays on the surface of an accretion disk by simultaneously solving the equations of radiative transfer, energy balance, and ionization equilibrium over a large range of column densities. We assume plane-parallel geometry and azimuthal symmetry, such that each calculation corresponds to a ring at a given distance from the central object. Our models include recent and complete atomic data for K-shell processes of the iron and oxygen isonuclear sequences. We examine the effect on the spectrum of fluorescent Kα line emission and absorption in the emitted spectrum. We also explore the dependence of the spectrum on the strength of the incident X-rays and other input parameters, and discuss the importance of Comptonization on the emitted spectrum.

Draft Genome Sequences of Three β-Lactam-Catabolizing Soil Proteobacteria

DEFF Research Database (Denmark)

Crofts, Terence S.; Wang, Bin; Spivak, Aaron

2017-01-01

Most antibiotics are derived from the soil, but their catabolism there, which is necessary to close the antibiotic carbon cycle, remains uncharacterized. We report the first draft genome sequences of soil Proteobacteria identified for subsisting solely on β-lactams as their carbon sources...

First-principles study of high-conductance DNA sequencing with carbon nanotube electrodes

KAUST Repository

Chen, X.

2012-03-26

Rapid and cost-effective DNA sequencing at the single nucleotide level might be achieved by measuring a transverse electronic current as single-stranded DNA is pulled through a nanometer-sized pore. In order to enhance the electronic coupling between the nucleotides and the electrodes and hence the current signals, we employ a pair of single-walled close-ended (6,6) carbon nanotubes (CNTs) as electrodes. We then investigate the electron transport properties of nucleotides sandwiched between such electrodes by using first-principles quantum transport theory. In particular, we consider the extreme case where the separation between the electrodes is the smallest possible that still allows the DNA translocation. The benzene-like ring at the end cap of the CNT can strongly couple with the nucleobases and therefore it can both reduce conformational fluctuations and significantly improve the conductance. As such, when the electrodes are closely spaced, the nucleobases can pass through only with their base plane parallel to the plane of CNT end caps. The optimal molecular configurations, at which the nucleotides strongly couple to the CNTs, and which yield the largest transmission, are first identified. These correspond approximately to the lowest energy configurations. Then the electronic structures and the electron transport of these optimal configurations are analyzed. The typical tunneling currents are of the order of 50 nA for voltages up to 1 V. At higher bias, where resonant transport through the molecular states is possible, the current is of the order of several μA. Below 1 V, the currents associated to the different nucleotides are consistently distinguishable, with adenine having the largest current, guanine the second largest, cytosine the third and, finally, thymine the smallest. We further calculate the transmission coefficient profiles as the nucleotides are dragged along the DNA translocation path and investigate the effects of configurational variations

INTERACTION OF CARBON DIOXIDE WITH CARBON ADSORBENTS BELOW 400 C

Energy Technology Data Exchange (ETDEWEB)

Deitz, V R; Carpenter, F G; Arnold, R G

1963-06-15

The adsorption of carbon dioxide on carbon adsorbents (FT carbon, coconut charcoal, acid-washed bone char) and adsorbents containing basic calcium phosphate (hydroxylapatite, bone char, ash of bone char) was studied. Special consideration was given to the pretreatment of the materials. The carbons equilibrated as rapidly as the temperature; the basic calcium phosphates showed a rapid initial adsorption followed by a very slow rate which continued for days. Linear adsorption isotherms were found on FT carbon and the isosteric heats varied slightiy with coverage. The isotherms for the remaining materials had varying curvature and were for the most part in the same sequence as the estimated surface areas. The isosteric heats of carbon dioxide correlated very well with the magnitude of surface hydroxyl groups, an estimate of which was made from the chemical composition. There appeared to be three increasing levels of interaction: (1) pure physical adsorption; (2) an adsorption complex having 'bicarbonate structure'; and (3) an adsorption complex having 'carbonate structure'. (auth)

Agaricus bisporus genome sequence: a commentary.

Science.gov (United States)

Kerrigan, Richard W; Challen, Michael P; Burton, Kerry S

2013-06-01

The genomes of two isolates of Agaricus bisporus have been sequenced recently. This soil-inhabiting fungus has a wide geographical distribution in nature and it is also cultivated in an industrialized indoor process ($4.7bn annual worldwide value) to produce edible mushrooms. Previously this lignocellulosic fungus has resisted precise econutritional classification, i.e. into white- or brown-rot decomposers. The generation of the genome sequence and transcriptomic analyses has revealed a new classification, 'humicolous', for species adapted to grow in humic-rich, partially decomposed leaf material. The Agaricus biporus genomes contain a collection of polysaccharide and lignin-degrading genes and more interestingly an expanded number of genes (relative to other lignocellulosic fungi) that enhance degradation of lignin derivatives, i.e. heme-thiolate peroxidases and β-etherases. A motif that is hypothesized to be a promoter element in the humicolous adaptation suite is present in a large number of genes specifically up-regulated when the mycelium is grown on humic-rich substrate. The genome sequence of A. bisporus offers a platform to explore fungal biology in carbon-rich soil environments and terrestrial cycling of carbon, nitrogen, phosphorus and potassium. Copyright © 2013 Elsevier Inc. All rights reserved.

Latest Permian carbonate carbon isotope variability traces heterogeneous organic carbon accumulation and authigenic carbonate formation

Science.gov (United States)

Schobben, Martin; van de Velde, Sebastiaan; Gliwa, Jana; Leda, Lucyna; Korn, Dieter; Struck, Ulrich; Vinzenz Ullmann, Clemens; Hairapetian, Vachik; Ghaderi, Abbas; Korte, Christoph; Newton, Robert J.; Poulton, Simon W.; Wignall, Paul B.

2017-11-01

Bulk-carbonate carbon isotope ratios are a widely applied proxy for investigating the ancient biogeochemical carbon cycle. Temporal carbon isotope trends serve as a prime stratigraphic tool, with the inherent assumption that bulk micritic carbonate rock is a faithful geochemical recorder of the isotopic composition of seawater dissolved inorganic carbon. However, bulk-carbonate rock is also prone to incorporate diagenetic signals. The aim of the present study is to disentangle primary trends from diagenetic signals in carbon isotope records which traverse the Permian-Triassic boundary in the marine carbonate-bearing sequences of Iran and South China. By pooling newly produced and published carbon isotope data, we confirm that a global first-order trend towards depleted values exists. However, a large amount of scatter is superimposed on this geochemical record. In addition, we observe a temporal trend in the amplitude of this residual δ13C variability, which is reproducible for the two studied regions. We suggest that (sub-)sea-floor microbial communities and their control on calcite nucleation and ambient porewater dissolved inorganic carbon δ13C pose a viable mechanism to induce bulk-rock δ13C variability. Numerical model calculations highlight that early diagenetic carbonate rock stabilization and linked carbon isotope alteration can be controlled by organic matter supply and subsequent microbial remineralization. A major biotic decline among Late Permian bottom-dwelling organisms facilitated a spatial increase in heterogeneous organic carbon accumulation. Combined with low marine sulfate, this resulted in varying degrees of carbon isotope overprinting. A simulated time series suggests that a 50 % increase in the spatial scatter of organic carbon relative to the average, in addition to an imposed increase in the likelihood of sampling cements formed by microbial calcite nucleation to 1 out of 10 samples, is sufficient to induce the observed signal of carbon

Latest Permian carbonate carbon isotope variability traces heterogeneous organic carbon accumulation and authigenic carbonate formation

Directory of Open Access Journals (Sweden)

M. Schobben

2017-11-01

Full Text Available Bulk-carbonate carbon isotope ratios are a widely applied proxy for investigating the ancient biogeochemical carbon cycle. Temporal carbon isotope trends serve as a prime stratigraphic tool, with the inherent assumption that bulk micritic carbonate rock is a faithful geochemical recorder of the isotopic composition of seawater dissolved inorganic carbon. However, bulk-carbonate rock is also prone to incorporate diagenetic signals. The aim of the present study is to disentangle primary trends from diagenetic signals in carbon isotope records which traverse the Permian–Triassic boundary in the marine carbonate-bearing sequences of Iran and South China. By pooling newly produced and published carbon isotope data, we confirm that a global first-order trend towards depleted values exists. However, a large amount of scatter is superimposed on this geochemical record. In addition, we observe a temporal trend in the amplitude of this residual δ13C variability, which is reproducible for the two studied regions. We suggest that (sub-sea-floor microbial communities and their control on calcite nucleation and ambient porewater dissolved inorganic carbon δ13C pose a viable mechanism to induce bulk-rock δ13C variability. Numerical model calculations highlight that early diagenetic carbonate rock stabilization and linked carbon isotope alteration can be controlled by organic matter supply and subsequent microbial remineralization. A major biotic decline among Late Permian bottom-dwelling organisms facilitated a spatial increase in heterogeneous organic carbon accumulation. Combined with low marine sulfate, this resulted in varying degrees of carbon isotope overprinting. A simulated time series suggests that a 50 % increase in the spatial scatter of organic carbon relative to the average, in addition to an imposed increase in the likelihood of sampling cements formed by microbial calcite nucleation to 1 out of 10 samples, is sufficient to induce the

GENOME-ENABLED DISCOVERY OF CARBON SEQUESTRATION GENES IN POPLAR

Energy Technology Data Exchange (ETDEWEB)

DAVIS J M

2007-10-11

Plants utilize carbon by partitioning the reduced carbon obtained through photosynthesis into different compartments and into different chemistries within a cell and subsequently allocating such carbon to sink tissues throughout the plant. Since the phytohormones auxin and cytokinin are known to influence sink strength in tissues such as roots (Skoog & Miller 1957, Nordstrom et al. 2004), we hypothesized that altering the expression of genes that regulate auxin-mediated (e.g., AUX/IAA or ARF transcription factors) or cytokinin-mediated (e.g., RR transcription factors) control of root growth and development would impact carbon allocation and partitioning belowground (Fig. 1 - Renewal Proposal). Specifically, the ARF, AUX/IAA and RR transcription factor gene families mediate the effects of the growth regulators auxin and cytokinin on cell expansion, cell division and differentiation into root primordia. Invertases (IVR), whose transcript abundance is enhanced by both auxin and cytokinin, are critical components of carbon movement and therefore of carbon allocation. Thus, we initiated comparative genomic studies to identify the AUX/IAA, ARF, RR and IVR gene families in the Populus genome that could impact carbon allocation and partitioning. Bioinformatics searches using Arabidopsis gene sequences as queries identified regions with high degrees of sequence similarities in the Populus genome. These Populus sequences formed the basis of our transgenic experiments. Transgenic modification of gene expression involving members of these gene families was hypothesized to have profound effects on carbon allocation and partitioning.

Syntheses of protoporphyrin-IX regioselectivity carbon-13 labelled at the alpha-vinyl carbons

International Nuclear Information System (INIS)

Smith, K.M.; Fujinari, E.M.

1986-01-01

A method for transformation of readily available beta-vinyl 99% carbon-13 enriched derivatives of protoporphyrin-IX dimethyl ester into the less accessible alpha-vinyl labelled isomers is described. The procedure involves thallium(III) promoted vinyl carbon rearrangement, and proceeds through 2,2-dimethoxyethyl, formylmethyl, 2-hydroxyethyl and 2-chloroethyl porphyrins; the rearranged vinyl groups are regenerated from 2-chloroethyl in the last step by treatment with base. No evidence of vinyl carbon scrambling in the sequence is observed, and spectroscopic data of the products are given. (author)

Complete genome sequence of the aerobic facultative methanotroph Methylocella silvestris BL2.

Science.gov (United States)

Chen, Yin; Crombie, Andrew; Rahman, M Tanvir; Dedysh, Svetlana N; Liesack, Werner; Stott, Matthew B; Alam, Maqsudul; Theisen, Andreas R; Murrell, J Colin; Dunfield, Peter F

2010-07-01

Methylocella silvestris BL2 is an aerobic methanotroph originally isolated from an acidic forest soil in Germany. It is the first fully authenticated facultative methanotroph. It grows not only on methane and other one-carbon (C(1)) substrates, but also on some compounds containing carbon-carbon bonds, such as acetate, pyruvate, propane, and succinate. Here we report the full genome sequence of this bacterium.

Removal of absorbable organic halides (aox) from recycled paper mill effluent using granular activated carbon-sequencing batch biofilm reactor (GAC-SBBR)

International Nuclear Information System (INIS)

Mohamad, A.B.; Rahman, R.A.; Kadhum, A.A.H.; Abdullah, S.R.S.; Shaari, S.

2006-01-01

Paper mills generate varieties of pollutants depending upon the type of the pulping process. Paper mill wastewaters have high chemical oxygen demand (COD) and colour, indicating high concentrations of recalcitrant organics. The study was conducted employing a Granular Activated Carbon - Sequencing Batch Biofilm Reactor (GAC-SBBR), containing 3.0 L working volume, operated in aerobic condition and packed with 200 g/L of 2-3 mm granular activated carbon (coconut shells) as a medium for biofilm growth. For the first couple of month, the HRT was 36 hours and the HRT of this reactor was adjusted to 24 hours in order to evaluate the performance of the system. The treated wastewater sample for these studies came from a recycle paper factory from MNI Sdn Bhd with 4 different samples characteristics. The adsorbable organic halides (AOX) to be determined and treated were Pentachlorophenol (PCP), 2,3,4,5-Tetrachlorophenol (2,3,4,5-TeCP), 2,4,6-Trichlorophenol (2,4,6-TCP), 2,4-Dichlorophenol ( 2,4-DCP), 2-Chlorophenol (CP) and phenol. Results showed that, the biofilm attached onto granular activated carbon (GAC) could substantially remove these recalcitrant in the wastewater. More over, results from the studies showed that high removal was achieved by the biofilm SBR with 10-100% removal of AOX and depending on HRT. (Author)

Carbon isotope composition of intermediates of the starch-malate sequence and level of the crassulacean acid metabolism in leaves of Kalanchoe blossfeldiana Tom Thumb.

Science.gov (United States)

Deleens, E; Garnier-Dardart, J; Queiroz, O

1979-09-01

Isotype analyses were performed on biochemical fractions isolated from leaves of Kalanchoe blossfeldiana Tom Thumb. during aging under long days or short days. Irrespective of the age or photoperiodic conditions, the intermediates of the starch-malate sequence (starch, phosphorylated compounds and organic acids) have a level of (13)C higher than that of soluble sugars, cellulose and hemicellulose. In short days, the activity of the crassulacean acid metabolism pathway is predominant as compared to that of C3 pathway: leaves accumulate organic acids, rich in (13)C. In long days, the activity of the crassulacean acid metabolism pathway increases as the leaves age, remaining, however, relatively low as compared to that of C3 pathway: leaves accumulate soluble sugars, poor in (13)C. After photoperiodic change (long days→short days), isotopic modifications of starch and organic acids suggest evidence for a lag phase in the establishment of the crassulacean acid metabolism pathway specific to short days. The relative proportions of carbon from a C3-origin (RuBPC acitivity as strong discriminating step, isotope discrimination in vivo=20‰) or C4-origin (PEPC activity as weak discriminating step, isotope discrimination in vivo=4‰) present in the biochemical fractions were calculated from their δ(13)C values. Under long days, 30 to 70% versus 80 to 100% under short days, of the carbon of the intermediates linked to the starch-malate sequence, or CAM pathway (starch, phosphorylated compounds and organic acids), have a C4-origin. Products connected to the C3 pathway (free sugars, cellulose, hemicellulose) have 0 to 50% of their carbon, arising from reuptake of the C4 from malate, under long days versus 30 to 70% under short days.

Carbon isotopic record from Upper Devonian carbonates at Dongcun in Guilin, southern China, supporting the world-wide pattern of carbon isotope excursions during Frasnian-Famennian transition

Institute of Scientific and Technical Information of China (English)

无

2003-01-01

Two positive δ13C excursions are presented in records from the Frasnian-Famennian (F-F) marine carbonate sediments in Europe, America, Africa, and Australia, having been considered as a worldwide pattern, and attributed to enhanced organic carbon burial during the F-F biological mass extinction. However, this worldwide pattern has not been revealed from the well-deposited Late Devonian sequences in southern China. In this paper, a detailed investigation has been made on the Late Devonian section at Dongcun, Guilin, southern China to constrain perturbations in δ13C of carbonates in the F-F deposited sequence. The result from this section also indicates two positive δ13C excursions during the F-F transition. The first excursion with an amplitude of 1.5‰ occurred at the bottom of linguiformis Zone, later than the early excursion existing in the Late rhenana Zone of the Late Devonian profiles in other continents, especially, in central Europe. This difference has been expected to be a result as conodont Palmatolepis linguiformis occurred earlier in southern China than other sites. The second excursion with an amplitude of 2.1‰ is located at the F-F boundary, same as the records from other continents. This result strongly supports the view that two carbon isotope positive excursions during the F-F transition are common in carbonate sediments, resulting from worldwide increases of organic carbon burial intensity.

Basin analysis in the Southern Tethyan margin: Facies sequences, stratal pattern and subsidence history highlight extension-to-inversion processes in the Cretaceous Panormide carbonate platform (NW Sicily)

Science.gov (United States)

Basilone, Luca; Sulli, Attilio

2018-01-01

In the Mediterranean, the South-Tethys paleomargin experienced polyphased tectonic episodes and paleoenvironmental perturbations during Mesozoic time. The Cretaceous shallow-water carbonate successions of the Panormide platform, outcropping in the northern edge of the Palermo Mountains (NW Sicily), were studied by integrating facies and stratal pattern with backstripping analysis to recognize the tectonics vs. carbonate sedimentation interaction. The features of the Requienid limestone, including geometric configuration, facies sequence, lithological changes and significance of the top-unconformity, highlight that at the end of the Lower Cretaceous the carbonate platform was tectonically dismembered in various rotating fault-blocks. The variable trends of the subsidence curves testify to different responses, both uplift and downthrow, of various platform-blocks impacted by extensional tectonics. Physical stratigraphic and facies analysis of the Rudistid limestone highlight that during the Upper Cretaceous the previously carbonate platform faulted-blocks were subjected to vertical movements in the direction opposite to the displacement produced by the extensional tectonics, indicating a positive tectonic inversion. Comparisons with other sectors of the Southern Tethyan and Adria paleomargins indicate that during the Cretaceous these areas underwent the same extensional and compressional stages occurring in the Panormide carbonate platform, suggesting a regional scale significance, in time and kinematics, for these tectonic events.

Experimental and Numerical Studies on Fiber Deformation and Formability in Thermoforming Process Using a Fast-Cure Carbon Prepreg: Effect of Stacking Sequence and Mold Geometry

Directory of Open Access Journals (Sweden)

Daeryeong Bae

2018-05-01

Full Text Available A fast-cure carbon fiber/epoxy prepreg was thermoformed against a replicated automotive roof panel mold (square-cup to investigate the effect of the stacking sequence of prepreg layers with unidirectional and plane woven fabrics and mold geometry with different drawing angles and depths on the fiber deformation and formability of the prepreg. The optimum forming condition was determined via analysis of the material properties of epoxy resin. The non-linear mechanical properties of prepreg at the deformation modes of inter- and intra-ply shear, tensile and bending were measured to be used as input data for the commercial virtual forming simulation software. The prepreg with a stacking sequence containing the plain-woven carbon prepreg on the outer layer of the laminate was successfully thermoformed against a mold with a depth of 20 mm and a tilting angle of 110°. Experimental results for the shear deformations at each corner of the thermoformed square-cup product were compared with the simulation and a similarity in the overall tendency of the shear angle in the path at each corner was observed. The results are expected to contribute to the optimization of parameters on materials, mold design and processing in the thermoforming mass-production process for manufacturing high quality automotive parts with a square-cup geometry.

Experimental and Numerical Studies on Fiber Deformation and Formability in Thermoforming Process Using a Fast-Cure Carbon Prepreg: Effect of Stacking Sequence and Mold Geometry

Science.gov (United States)

Bae, Daeryeong; Kim, Shino; Lee, Wonoh; Yi, Jin Woo; Um, Moon Kwang; Seong, Dong Gi

2018-01-01

A fast-cure carbon fiber/epoxy prepreg was thermoformed against a replicated automotive roof panel mold (square-cup) to investigate the effect of the stacking sequence of prepreg layers with unidirectional and plane woven fabrics and mold geometry with different drawing angles and depths on the fiber deformation and formability of the prepreg. The optimum forming condition was determined via analysis of the material properties of epoxy resin. The non-linear mechanical properties of prepreg at the deformation modes of inter- and intra-ply shear, tensile and bending were measured to be used as input data for the commercial virtual forming simulation software. The prepreg with a stacking sequence containing the plain-woven carbon prepreg on the outer layer of the laminate was successfully thermoformed against a mold with a depth of 20 mm and a tilting angle of 110°. Experimental results for the shear deformations at each corner of the thermoformed square-cup product were compared with the simulation and a similarity in the overall tendency of the shear angle in the path at each corner was observed. The results are expected to contribute to the optimization of parameters on materials, mold design and processing in the thermoforming mass-production process for manufacturing high quality automotive parts with a square-cup geometry. PMID:29883413

Complete Genome Sequence of the Aerobic Facultative Methanotroph Methylocella silvestris BL2▿

Science.gov (United States)

Chen, Yin; Crombie, Andrew; Rahman, M. Tanvir; Dedysh, Svetlana N.; Liesack, Werner; Stott, Matthew B.; Alam, Maqsudul; Theisen, Andreas R.; Murrell, J. Colin; Dunfield, Peter F.

2010-01-01

Methylocella silvestris BL2 is an aerobic methanotroph originally isolated from an acidic forest soil in Germany. It is the first fully authenticated facultative methanotroph. It grows not only on methane and other one-carbon (C1) substrates, but also on some compounds containing carbon-carbon bonds, such as acetate, pyruvate, propane, and succinate. Here we report the full genome sequence of this bacterium. PMID:20472789

Complete Genome Sequence of the Aerobic Facultative Methanotroph Methylocella silvestris BL2▿

OpenAIRE

Chen, Yin; Crombie, Andrew; Rahman, M. Tanvir; Dedysh, Svetlana N.; Liesack, Werner; Stott, Matthew B.; Alam, Maqsudul; Theisen, Andreas R.; Murrell, J. Colin; Dunfield, Peter F.

2010-01-01

Methylocella silvestris BL2 is an aerobic methanotroph originally isolated from an acidic forest soil in Germany. It is the first fully authenticated facultative methanotroph. It grows not only on methane and other one-carbon (C1) substrates, but also on some compounds containing carbon-carbon bonds, such as acetate, pyruvate, propane, and succinate. Here we report the full genome sequence of this bacterium.

SAXS study on activated carbons

International Nuclear Information System (INIS)

Bota, A.; Heringer, D.; Mihalffy, T.

1999-01-01

SAXS fractal analysis of activated carbons is presented. It gives very useful information about the structural changes of the carbon skeleton. From the fact, that the sequence of the activation and the heat treatment affect the fractal behaviours more drastically than the particle size distribution of the structural units, it follows that all changes in the pore and matrix structure may reduce principally to the bonding of the crystallite units. (K.A.)

Application of carbon isotope stratigraphy to late miocene shallow marine sediments, new zealand.

Science.gov (United States)

Loutit, T S; Kennett, J P

1979-06-15

A distinct (0.5 per mil) carbon-13/carbon-12 isotopic shift in the light direction has been identified in a shallow marine sedimentary sequence of Late Miocene age at Blind River, New Zealand, and correlated with a similar shift in Late Miocene Deep Sea Drilling Project sequences throughout the Indo-Pacific. A dated piston core provides an age for the shift of 6.2 +/- 0.1 million years. Correlations based on the carbon isotopic change require a revision of the previously established magnetostratigraphy at Blind River. The carbon shift at Blind River occurs between 6.2 and 6.3 +/- 0.1 million years before present. A new chronology provides an age for the evolutionary first appearance datum of Globorotalia conomiozea at 6.1 +/- 0.1 million years, the beginning of a distinct latest Miocene cooling event associated with the Kapitean stage at 6.2 +/- 0.1 million years, and the beginning of a distinct shallowing of water depths at 6.1 +/- 0.1 million years. The Miocene-Pliocene boundary as recognized in New Zealand is now dated at 5.3 +/- 0.1 million years. Extension of carbon isotope stratigraphy to other shallow Late Miocene sequences should provide an important datum for international correlation of Late Miocene shallow and deep marine sequences.

Characterization of carbon ion-induced mutations in Arabidopsis thaliana

International Nuclear Information System (INIS)

Shikazono, N.; Suzuki, C.; Kitamura, S.; Watanabe, H.; Tano, S.; Tanaka, A.

2003-01-01

Full text: Irradiation of Arabidopsis thaliana by carbon ions was carried out to investigate the mutational effect of ion particles in higher plants. The averaged mutation rate of carbon ions was 2.0 X 10 -6 / Gy, which was 18-fold higher than that of electrons. PCR analysis of the carbon ion-induced mutants showed that, out of 28 mutant alleles, 14 had point-like mutations within the gene, while 14 contained large structural alterations. In the case of 12 electron-induced mutants, 9 had point-like mutations within the gene, while 3 contained large structural alterations. These results suggest that carbon ions are more likely to induce large structural alterations compared with electrons. Further sequence analysis revealed that most of the point-like mutations induced by carbon ions were short deletions. In the case of rearrangements, DNA strand breaks were found to be rejoined using, if present, short homologous sequences for both types of radiation. After carbon ion-irradiation, small deletions were frequently observed around the breakpoints, whereas duplications of terminal sequence were found after electron-irradiation. These results suggest that non-homologous end joining (NHEJ) pathway operates after plant cells are exposed to both ion particles and electrons but that different mode of rejoining deals with the broken ends produced by each radiation. From the present results, it seems reasonable to assume that carbon ions could predominantly induce null mutations in Arabidopsis. The fact that the molecular nature of carbon ion-induced mutation was different from that of electrons and that the molecular mechanisms of cells to induce mutations appeared to be also different implicates that ion particle is not only valuable as a new mutagen but also useful as a new tool to study repair mechanisms of certain types of DNA damage

[Characterization of Black and Dichothrix Cyanobacteria Based on the 16S Ribosomal RNA Gene Sequence

Science.gov (United States)

Ortega, Maya

2010-01-01

My project focuses on characterizing different cyanobacteria in thrombolitic mats found on the island of Highborn Cay, Bahamas. Thrombolites are interesting ecosystems because of the ability of bacteria in these mats to remove carbon dioxide from the atmosphere and mineralize it as calcium carbonate. In the future they may be used as models to develop carbon sequestration technologies, which could be used as part of regenerative life systems in space. These thrombolitic communities are also significant because of their similarities to early communities of life on Earth. I targeted two cyanobacteria in my research, Dichothrix spp. and whatever black is, since they are believed to be important to carbon sequestration in these thrombolitic mats. The goal of my summer research project was to molecularly identify these two cyanobacteria. DNA was isolated from each organism through mat dissections and DNA extractions. I ran Polymerase Chain Reactions (PCR) to amplify the 16S ribosomal RNA (rRNA) gene in each cyanobacteria. This specific gene is found in almost all bacteria and is highly conserved, meaning any changes in the sequence are most likely due to evolution. As a result, the 16S rRNA gene can be used for bacterial identification of different species based on the sequence of their 16S rRNA gene. Since the exact sequence of the Dichothrix gene was unknown, I designed different primers that flanked the gene based on the known sequences from other taxonomically similar cyanobacteria. Once the 16S rRNA gene was amplified, I cloned the gene into specialized Escherichia coli cells and sent the gene products for sequencing. Once the sequence is obtained, it will be added to a genetic database for future reference to and classification of other Dichothrix sp.

Soil, vegetation and total organic carbon stock development in self-restoring abandoned vineyards

Science.gov (United States)

József Novák, Tibor; Incze, József; Spohn, Marie; Giani, Luise

2016-04-01

Abandoned vineyard's soil and vegetation development was studied on Tokaj Nagy-Hill, which is one of the traditional wine-producing regions of Hungary, it is declared as UNESCO World Heritage site as cultural landscape. Spatial distribution and pattern of vineyards were changing during the last several hundreds of years, therefore significant part of abandoned vineyards were subjected to long-term spontaneous secondary succession of vegetation and self-restoration of soils in absence of later cultivation. Two chronosequences of spontaneously regenerating vineyard abandonments, one on south (S-sequence) and one on southwest (SW-sequence) slope with differing times since their abandonment (193, 142, 101, 63, 39 and 14 years), were compiled and studied. The S-sequence was 25-35% sloped and strongly eroded, and the SW-sequence was 17-25% sloped and moderately eroded. The sites were investigated in respect of vegetation characteristics, soil physico-chemical characteristics, total organic carbon stocks (TOC stocks), accumulation rates of total organic carbon (TOC accumulation rates), and soil profiles, which were classified according to the World Reference Base (WRB) 2014. Vegetation development resulted in shrub-grassland mosaics, supplemented frequently by protected forb species and forest development at the earliest abandonment in S-sequence, and predominantly to forest vegetation in SW-sequence, where trees were only absent at the 63 and 14 years old abandonment sites. In all sites soils on level of reference groups according to WRB were classified, and Cambisols, Regosols, Calcisols, Leptosols, Chernozems and Phaeozems were found. Soils of the S-sequence show shallow remnants of loess cover with colluvic and redeposited soil materials containing 15-65% skeletal volcanic rock of weathering products coated by secondary calcium carbonates. The SW-sequence profiles are developed on deep loess or loess derivatives. The calcium-carbonate content was higher in profiles of

Influence of Layup Sequence on the Surface Accuracy of Carbon Fiber Composite Space Mirrors

Science.gov (United States)

Yang, Zhiyong; Liu, Qingnian; Zhang, Boming; Xu, Liang; Tang, Zhanwen; Xie, Yongjie

2018-04-01

Layup sequence is directly related to stiffness and deformation resistance of the composite space mirror, and error caused by layup sequence can affect the surface precision of composite mirrors evidently. Variation of layup sequence with the same total thickness of composite space mirror changes surface form of the composite mirror, which is the focus of our study. In our research, the influence of varied quasi-isotropic stacking sequences and random angular deviation on the surface accuracy of composite space mirrors was investigated through finite element analyses (FEA). We established a simulation model for the studied concave mirror with 500 mm diameter, essential factors of layup sequences and random angular deviations on different plies were discussed. Five guiding findings were described in this study. Increasing total plies, optimizing stacking sequence and keeping consistency of ply alignment in ply placement are effective to improve surface accuracy of composite mirror.

Carbon nanotubes field-effect transistor for rapid detection of DHA

International Nuclear Information System (INIS)

Nguyen Thi Thuy; Nguyen Duc Chien; Mai Anh Tuan

2012-01-01

This paper presents the development of DNA sensor based on a network carbon nanotubes field effect transistor (CNTFETs) for Escherichia coli bacteria detection. The DNA sequences were immobilized on single-walled carbon nanotubes of transistor CNTFETs by using absorption. The hybridization of the DNA probe sequences and complementary DNA strands was detected by electrical conductance change from the electron doping by DNA hybridization directly on the carbon nanotubes leading to the change in the metal-CNTs barrier energy through the modulation of the electrode work function of carbon nanotubes field effect transistor. The results showed that the response time of DNA sensor was approximately 1 min and the sensitivity of DNA sensor was at 0.565 μA/nM; the detection limit of the sensor was about 1 pM of E. coli bacteria sample. (author)

Path of Carbon in Photosynthesis III.

Science.gov (United States)

Benson, A. A.; Calvin, M.

1948-06-01

Although the overall reaction of photosynthesis can be specified with some degree of certainty (CO{sub 2} + H{sub 2}O + light {yields} sugars + possibly other reduced substances), the intermediates through which the carbon passes during the course of this reduction have, until now, been largely a matter of conjecture. The availability of isotopic carbon, that is, a method of labeling the carbon dioxide, provides the possibility of some very direct experiments designed to recognize these intermediates and, perhaps, help to understand the complex sequence and interplay of reactions which must constitute the photochemical process itself. The general design of such experiments is an obvious one, namely the exposure of the green plant to radioactive carbon dioxide and light under a variety of conditions and for continually decreasing lengths of time, followed by the identification of the compounds into which the radioactive carbon is incorporated under each condition and time period. From such data it is clear that in principle, at least, it should be possible to establish the sequence of compounds in time through which the carbon passes on its path from carbon dioxide to the final products. In the course of shortening the photosynthetic times, one times, one ultimately arrives at the condition of exposing the plants to the radioactive carbon dioxide with a zero illumination time, that is, in the dark. Actually, in the work the systematic order of events was reversed, and they have begun by studying first the dark fixation and then the shorter photosynthetic times. The results of the beginnings of this sort of a systematic investigation are given in Table I which includes three sets of experiments, namely a dark fixation experiment and two photosynthetic experiments, one of 30 seconds duration and the other of 60 seconds duration.

Depositional environments and sequence stratigraphy of the Bahram Formation (middle–late Devonian in north of Kerman, south-central Iran

Directory of Open Access Journals (Sweden)

Afshin Hashmie

2016-09-01

Full Text Available This study is focused on sedimentary environments, facies distribution, and sequence stratigraphy. The facies and sequence stratigraphic analyses of the Bahram Formation (middle–late Devonian in south-central Iran are based on two measured stratigraphic sections in the southern Tabas block. The Bahram Formation overlies red sandstones Padeha Formation in sections Hutk and Sardar and is overlain by Carboniferous carbonate deposits of Hutk Formation paraconformably, with a thickness of 354 and 386 m respectively. Mixed siliciclastic and carbonate sediments are present in this succession. The field observations and laboratory studies were used to identify 14 micro/petrofacies, which can be grouped into 5 depositional environments: shore, tidal flat, lagoon, shoal and shallow open marine. A mixed carbonate-detrital shallow shelf is suggested for the depositional environment of the Bahram Formation which deepens to the east (Sardar section and thins in southern locations (Hutk section. Three 3rd-order cyclic siliciclastic and carbonate sequences in the Bahram Formation and one sequence shared with the overlying joint with Hutk Formation are identified, on the basis of shallowing upward patterns in the micro/pertofacies.

Impact ejecta and carbonate sequence in the eastern sector of the Chicxulub crater

Science.gov (United States)

Urrutia-Fucugauchi, Jaime; Chavez-Aguirre, Jose Maria; Pérez-Cruz, Ligia; De la Rosa, Jose Luis

2008-12-01

The Chicxulub 200 km diameter crater located in the Yucatan platform of the Gulf of Mexico formed 65 Myr ago and has since been covered by Tertiary post-impact carbonates. The sediment cover and absence of significant volcanic and tectonic activity in the carbonate platform have protected the crater from erosion and deformation, making Chicxulub the only large multi-ring crater in which ejecta is well preserved. Ejecta deposits have been studied by drilling/coring in the southern crater sector and at outcrops in Belize, Quintana Roo and Campeche; little information is available from other sectors. Here, we report on the drilling/coring of a section of ˜34 m of carbonate breccias at 250 m depth in the Valladolid area (120 km away from crater center), which are interpreted as Chicxulub proximal ejecta deposits. The Valladolid breccias correlate with the carbonate breccias cored in the Peto and Tekax boreholes to the south and at similar radial distance. This constitutes the first report of breccias in the eastern sector close to the crater rim. Thickness of the Valladolid breccias is less than that at the other sites, which may indicate erosion of the ejecta deposits before reestablishment of carbonate deposition. The region east of the crater rim appears different from regions to the south and west, characterized by high density and scattered distribution of sinkholes.

Controls on declining carbon balance with leaf age among 10 woody species in Australian woodland: do leaves have zero daily net carbon balances when they die?

Science.gov (United States)

Reich, Peter B; Falster, Daniel S; Ellsworth, David S; Wright, Ian J; Westoby, Mark; Oleksyn, Jacek; Lee, Tali D

2009-01-01

* Here, we evaluated how increased shading and declining net photosynthetic capacity regulate the decline in net carbon balance with increasing leaf age for 10 Australian woodland species. We also asked whether leaves at the age of their mean life-span have carbon balances that are positive, zero or negative. * The net carbon balances of 2307 leaves on 53 branches of the 10 species were estimated. We assessed three-dimensional architecture, canopy openness, photosynthetic light response functions and dark respiration rate across leaf age sequences on all branches. We used YPLANT to estimate light interception and to model carbon balance along the leaf age sequences. * As leaf age increased to the mean life-span, increasing shading and declining photosynthetic capacity each separately reduced daytime carbon gain by approximately 39% on average across species. Together, they reduced daytime carbon gain by 64% on average across species. * At the age of their mean life-span, almost all leaves had positive daytime carbon balances. These per leaf carbon surpluses were of a similar magnitude to the estimated whole-plant respiratory costs per leaf. Thus, the results suggest that a whole-plant economic framework, including respiratory costs, may be useful in assessing controls on leaf longevity.

Carbon isotope variations in the upper Carboniferous - Permian Mallemuk Mountain Group, eastern North Greenland

International Nuclear Information System (INIS)

Stemmerik, L.; Magaritz, M.

1989-01-01

Isotope data from Late Palaeozoic limestones of the Wandel Sea Basin in eastern North Greenland show a variation of δ 13 C from 0.0 0/00 to 5.7 0/00 vs PDB. Carbonates depleted in 13 C occur in the basal part of lower Moscovian, upper Moscovian and middle Gzhelian transgressive sequences. 13 C enriched limestones occur later in the cycles. The most 13 C enriched limestones occur in the youngest (late Early Permian-early Late Permian) part of the sequence in Amdrup Land. The isotopic data is believed to represent changes in the global carbon cycle. Thus 13 C enriched carbonates correlate to periods of burial of organic carbon mostly as coal, while 13 C depleted carbonates formed as the result of erosion and oxidation of organic carbon during sea-level low stands. (author)

Sequence stratigraphy from ``spot'' outcrops—example from a carbonate-dominated setting: Devonian-Carboniferous transition, Dinant synclinorium (Belgium)

Science.gov (United States)

Van Steenwinkel, M.

1990-12-01

The application of sequence stratigraphy appears to be perfectly valid in isolated "spot" outcrops, which usually are badly exposed and located in areas of strong tectonic overprint. The case study presented here is in a carbonate-dominated setting at the northern edge of the Cornwall-Rhenish basin, during latest Devonian and earliest Carboniferous times. The approach taken involved the analysis of facies and vertical facies evolutions, in combination with detailed biostratigraphy. The subsequent deduction of deepening and shallowing events, and the understanding of the sedimentary response to these events in different palaeogeographical positions, are the basis for lateral correlation of facies sequences. A similar trend in the changes of deepenings and shallowings throughout the area, regardless of lateral facies differentiation, indicates a relationship between bathymetric changes and relative sea-level changes, that is independent of local differences in the sedimentation or subsidence rates. The studied stratigraphic interval, with its apparently "abrupt" changes in facies or lithology, is the sedimentary response to six, gradually changing trends in the rate of relative sea-level fall and rise. End-Devonian, offshore highstand deposits (1) are capped by an unconformity surface or by a surface of submarine erosion and nondeposition, representing a sequence boundary (2). The overlying lowstand unit consists of a basal (3) and an upper (4) part. The basal part contains an oolitic and crinoidal sand shoals, associated with a transgressive lag deposit in offshore position; the upper, main part is a prograding wedge of shallow-marine crinoidal sands, intercalated with increasingly deeper-water shaly facies (higher-order fluctuation). This lowstand unit was deposited during the initial, slow phase of relative sea-level rise. It levelled the topographic relief before the final drowning during the subsequent rapid (near the rise inflection point) relative sea

Metabolic diversity and ecological niches of Achromatium populations revealed with single-cell genomic sequencing

Directory of Open Access Journals (Sweden)

Muammar eMansor

2015-08-01

Full Text Available Large, sulfur-cycling, calcite-precipitating bacteria in the genus Achromatium represent a significant proportion of bacterial communities near sediment-water interfaces throughout the world. Our understanding of their potentially crucial roles in calcium, carbon, sulfur, nitrogen, and iron cycling is limited because they have not been cultured or sequenced using environmental genomics approaches to date. We utilized single-cell genomic sequencing to obtain one incomplete and two nearly complete draft genomes for Achromatium collected at Warm Mineral Springs, FL. Based on 16S rRNA gene sequences, the three cells represent distinct and relatively distant Achromatium populations (91-92% identity. The draft genomes encode key genes involved in sulfur and hydrogen oxidation; oxygen, nitrogen and polysulfide respiration; carbon and nitrogen fixation; organic carbon assimilation and storage; chemotaxis; twitching motility; antibiotic resistance; and membrane transport. Known genes for iron and manganese energy metabolism were not detected. The presence of pyrophosphatase and vacuolar (V-type ATPases, which are generally rare in bacterial genomes, suggests a role for these enzymes in calcium transport, proton pumping, and/or energy generation in the membranes of calcite-containing inclusions.

Linear series of stellar models. Pt. 4. Helium-carbon stars of 3.5Msub(o) and 1Msub(o)

International Nuclear Information System (INIS)

Kozlowski, M.; Paczynski, B.; Popova, K.

1973-01-01

One linear series of models for a star of 3.5Msub(o) and two linear series of models for a star of 1Msub(o) are constructed. Models consist of helium rich envelopes (Y = 0.97, Z = 0.03) and pure carbon cores, and they have a rectangular helium profile, Y(Msub(r)). The linear series for a star of 3.5Msub(o) begins on the normal branch of the helium main sequence and terminates on the normal branch of the carbon main sequence. This series has eight turning points at which the core mass attains a local extremum. One of the two linear series for a star of 1Msub(o) begins on the normal branch of the helium main sequence, terminates on the high density branch of the helium main sequence, and has one turning point. The second linear series for a star of 1Msub(o) begins on the normal branch of the carbon main sequence, terminates on the high density branch of the carbon main sequence, and has three turning points. Two such linear series may have a common bifurcation point for a star of about 1.26Msub(o). (author)

Carbon-13 NMR characterization of actinyl(VI) carbonate complexes in aqueous solution

International Nuclear Information System (INIS)

Clark, D.L.; Hobart, D.E.; Palmer, P.D.; Sullivan, J.C.; Stout, B.E.

1992-01-01

The uranyl(VI) carbonate system has been re-examined using 13 C NMR of 99.9% 13 C-enriched U VI O 2 ( 13 CO 3 ) 3 4- in millimolar concentrations. By careful control of carbonate ion concentration, we have confirmed the existence of the trimer, and observed dynamic equilibrium between the monomer and the timer. In addition, the ligand exchange reaction between free and coordinated carbonate on Pu VI O 2 ( 13 CO 3 ) 3 4- and Am VI O 2 ( 13 CO 3 ) 3 4- systems has been examined by variable temperature 13 C NMR line-broadening techniques 13 C NMR line-broadening techniques. A modified Carr-Purcell-Meiboom-Gill NMR pulse sequence was written to allow for experimental determination of ligand exchange parameters for paramagnetic actinide complexes. Preliminary Eyring analysis has provided activation parameters of ΔG double-dagger 295 = 56 kJ/M, ΔH double-dagger = 38 kJ/M, and ΔS double-dagger = -60 J/M-K for the plutonyl triscarbonate system, suggesting an associative transition state for the plutonyl (VI) carbonate complex self-exchange reaction. Experiments for determination of the activation parameters for the americium (VI) carbonate system are in progress

THE INFRARED SPECTRAL PROPERTIES OF MAGELLANIC CARBON STARS

Energy Technology Data Exchange (ETDEWEB)

Sloan, G. C. [Cornell Center for Astrophysics and Planetary Science, Cornell Univ., Ithaca, NY 14853-6801 (United States); Kraemer, K. E. [Institute for Scientific Research, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467 (United States); McDonald, I.; Zijlstra, A. A. [Jodrell Bank Centre for Astrophysics, Univ. of Manchester, Manchester M13 9PL (United Kingdom); Groenewegen, M. A. T. [Koninklijke Sterrenwacht van België, Ringlaan 3, B-1180 Brussels (Belgium); Wood, P. R. [Research School of Astronomy and Astrophysics, Australian National University, Canberra, ACT 2611 (Australia); Lagadec, E. [Observatoire de la Côte d’Azur, F-06300, Nice (France); Boyer, M. L. [CRESST and Observational Cosmology Lab, Code 665, NASA Goddard Space Flight Center, Greenbelt, MD, 20771 (United States); Kemper, F.; Srinivasan, S. [Academia Sinica, Institute of Astronomy and Astrophysics, 11F Astronomy-Mathematics Building, NTU/AS, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan, R.O.C. (China); Matsuura, M. [School of Physics and Astronomy, Cardiff University, Queen’s Buildings, The Parade, Cardiff, CF24 3AA (United Kingdom); Sahai, R. [Jet Propulsion Laboratory, California Institute of Technology, MS 183-900, Pasadena, CA 91109 (United States); Sargent, B. A. [Center for Imaging Science and Laboratory for Multiwavelength Astrophysics, Rochester Institute of Technology, 54 Lomb Memorial Drive, Rochester, NY 14623 (United States); Van Loon, J. Th. [Lennard Jones Laboratories, Keele University, Staffordshire ST5 5BG (United Kingdom); Volk, K., E-mail: sloan@isc.astro.cornell.edu [Space Telescope Science Institute, 3700 San Martin Dr., Baltimore, MD 21218 (United States)

2016-07-20

The Infrared Spectrograph on the Spitzer Space Telescope observed 184 carbon stars in the Magellanic Clouds. This sample reveals that the dust-production rate (DPR) from carbon stars generally increases with the pulsation period of the star. The composition of the dust grains follows two condensation sequences, with more SiC condensing before amorphous carbon in metal-rich stars, and the order reversed in metal-poor stars. MgS dust condenses in optically thicker dust shells, and its condensation is delayed in more metal-poor stars. Metal-poor carbon stars also tend to have stronger absorption from C{sub 2}H{sub 2} at 7.5 μ m. The relation between DPR and pulsation period shows significant apparent scatter, which results from the initial mass of the star, with more massive stars occupying a sequence parallel to lower-mass stars, but shifted to longer periods. Accounting for differences in the mass distribution between the carbon stars observed in the Small and Large Magellanic Clouds reveals a hint of a subtle decrease in the DPR at lower metallicities, but it is not statistically significant. The most deeply embedded carbon stars have lower variability amplitudes and show SiC in absorption. In some cases they have bluer colors at shorter wavelengths, suggesting that the central star is becoming visible. These deeply embedded stars may be evolving off of the asymptotic giant branch and/or they may have non-spherical dust geometries.

THE INFRARED SPECTRAL PROPERTIES OF MAGELLANIC CARBON STARS

International Nuclear Information System (INIS)

Sloan, G. C.; Kraemer, K. E.; McDonald, I.; Zijlstra, A. A.; Groenewegen, M. A. T.; Wood, P. R.; Lagadec, E.; Boyer, M. L.; Kemper, F.; Srinivasan, S.; Matsuura, M.; Sahai, R.; Sargent, B. A.; Van Loon, J. Th.; Volk, K.

2016-01-01

The Infrared Spectrograph on the Spitzer Space Telescope observed 184 carbon stars in the Magellanic Clouds. This sample reveals that the dust-production rate (DPR) from carbon stars generally increases with the pulsation period of the star. The composition of the dust grains follows two condensation sequences, with more SiC condensing before amorphous carbon in metal-rich stars, and the order reversed in metal-poor stars. MgS dust condenses in optically thicker dust shells, and its condensation is delayed in more metal-poor stars. Metal-poor carbon stars also tend to have stronger absorption from C 2 H 2 at 7.5 μ m. The relation between DPR and pulsation period shows significant apparent scatter, which results from the initial mass of the star, with more massive stars occupying a sequence parallel to lower-mass stars, but shifted to longer periods. Accounting for differences in the mass distribution between the carbon stars observed in the Small and Large Magellanic Clouds reveals a hint of a subtle decrease in the DPR at lower metallicities, but it is not statistically significant. The most deeply embedded carbon stars have lower variability amplitudes and show SiC in absorption. In some cases they have bluer colors at shorter wavelengths, suggesting that the central star is becoming visible. These deeply embedded stars may be evolving off of the asymptotic giant branch and/or they may have non-spherical dust geometries.

IRAS colors of carbon stars - An optical spectroscopic test

International Nuclear Information System (INIS)

Cohen, M.; Wainscoat, R.J.; Walker, H.J.; Volk, K.; Schwartz, D.E.

1989-01-01

Optical spectra are obtained of 57 photographic counterparts to IRAS sources not previously studied spectroscopically, and expected on the basis of their IRAS colors to be M or C type stars. Confirmed carbon stars are found only in a restricted range of 12-25 index, and constitute a striking vertical sequence in the 12-25-60 micron color-color diagram. This sequence is in accord with evolutionary models for AGB stars that convert M into C stars by dredge-up, and follow loops in the color-color plane. Optically visible and optically invisible carbon stars occupy different color-color locations consistent with their representations of different evolutionary states in the life of relatively low-mass stars. 16 refs

Microfacies characteristics, sedimentary environments and sequence stratigraphy of Upper Cretaceous deposits in northwest of Nehbandan (Basiran section

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Mohammad nabi Gorgij

2015-10-01

Full Text Available Introduction   The Basiran stratigraphic section is located about 160 km northwest of Nehbandan.The section was measured in detail at 59 06 30 N and 31 52 50 E. Nehbandan area with respect to fourfold geological subdivision of Iran is part of Central Iran that is located in the eastern flank of Lut Block which first time are studied by Stocklin et al.in 1972. Gorgij (2001 stratigraphically and paleontologically investigate Upper Cretaceous deposits in Mighan and Basiran sections. Upper Cretaceous deposits in in this area consists of 275m conglomerate,alternation of conglomerate-sandstone, sandy limestone -marl and limy marl, marl with intercalation of limestone-sandy limestone thin beds and medium-bedded to massive limestone. Microfacies analysis led to the recognition of 9 microfacies that are related to 5 belts; Coast, tidal flat, lagoon, shoal, shallow open marine and deep open marine environments. Main part of the section are deposited in the open marine environment that consist of marl,marly limestone and limestone. The doals of this study are : (1 describing and determining main carbonate and siliciclastic microfacies of late Cretaceous deposits (2 interpreting and providing depositional model for reconstruction of its paleoenvironmental setting based on microfacies characteristics (3 dividing the section based on lithostratigraphic principles and (4 recognizing a sequence stratigraphic model of this successions based on the vertical variation of facies,stratal key beds and stratal packing pattern.       Material and Method   The Basiran section as a complete stratigraphic section was measured and described. Up to 68 samples (indicated by KB1 to KB68 were collected and 170 thin sections are prepared. Based on field observations, sedimentological characteristics, parasequence stacking patterns, sequence boundary types and other key stratigraphical surfaces are identified and were obtained. Scheme of Dunham (1962 and Embry and Klovan

Microfacies characteristics, sedimentary environments and sequence stratigraphy of Upper Cretaceous deposits in northwest of Nehbandan (Basiran section

Directory of Open Access Journals (Sweden)

Azadeh Bordbar

2015-09-01

Full Text Available   Introduction   The Basiran stratigraphic section is located about 160 km northwest of Nehbandan.The section was measured in detail at 59 06 30 N and 31 52 50 E. Nehbandan area with respect to fourfold geological subdivision of Iran is part of Central Iran that is located in the eastern flank of Lut Block which first time are studied by Stocklin et al.in 1972. Gorgij (2001 stratigraphically and paleontologically investigate Upper Cretaceous deposits in Mighan and Basiran sections. Upper Cretaceous deposits in in this area consists of 275m conglomerate,alternation of conglomerate-sandstone, sandy limestone -marl and limy marl, marl with intercalation of limestone-sandy limestone thin beds and medium-bedded to massive limestone. Microfacies analysis led to the recognition of 9 microfacies that are related to 5 belts Coast, tidal flat, lagoon, shoal, shallow open marine and deep open marine environments. Main part of the section are deposited in the open marine environment that consist of marl,marly limestone and limestone. The doals of this study are : (1 describing and determining main carbonate and siliciclastic microfacies of late Cretaceous deposits (2 interpreting and providing depositional model for reconstruction of its paleoenvironmental setting based on microfacies characteristics (3 dividing the section based on lithostratigraphic principles and (4 recognizing a sequence stratigraphic model of this successions based on the vertical variation of facies,stratal key beds and stratal packing pattern.       Material and Method   The Basiran section as a complete stratigraphic section was measured and described. Up to 68 samples (indicated by KB1 to KB68 were collected and 170 thin sections are prepared. Based on field observations, sedimentological characteristics, parasequence stacking patterns, sequence boundary types and other key stratigraphical surfaces are identified and were obtained. Scheme of Dunham (1962 and Embry

Impacts of extreme weather events and climate variability on carbon exchanges in an age-sequence of managed temperate pine forests from 2003 to 201

Science.gov (United States)

Arain, M. A.

2017-12-01

North American temperate forests are a critical component of the global carbon cycle and regional water resources. A large portion of these forests has traditionally been managed for timber production and other uses. The response of these forests, which are in different stages of development, to extreme weather events such as drought and heat stresses, climate variability and management regimes is not fully understood. In this study, eddy covariance flux measurements in an age sequence (77-, 42-, and 14-years old as of 2016) of white pine (Pinus strobus L.) plantation forests in southern Ontario, Canada are examined to determine the impact of heat and drought stresses and climate variability over a 14 year period (2003 to 2016). The mean annual net ecosystem productivity (NEP) values were 195 ± 87, 512 ±161 and 103 ± 103 g C m-2 year-1 in 77-, 42- and 14-year-old forests respectively, over the study period. The youngest forest became a net carbon sink in the fifth year of its growth. Air temperature was a dominant control on carbon fluxes and heat stress reduced photosynthesis much more as compared to ecosystem respiration in the growing season. A large decrease in annual NEP was observed during years experiencing heat waves. Drought stress had the strongest impact on the middle age forest which had the largest carbon sink and water demand. In contrast, young forest was more sensitive to heat stress, than drought. Severity of heat and drought stress impacts was highly dependent on the timing of these events. Simultaneous occurrence of heat and drought stress in the early growing season such as in 2012 and 2016 had a drastic negative impact on carbon balance in these forests due to plant-soil-atmosphere feedbacks. Future research should consider the timing of the extreme events, the stage of forest development and effects of extreme events on component fluxes. This research helps to assess the vulnerability of managed forests and their ecological and hydrological

Welding distortion analysis of multipass joint combination with different sequences using 3D FEM and experiment

International Nuclear Information System (INIS)

Manurung, Yupiter H.P.; Lidam, Robert Ngendang; Rahim, M. Ridzwan; Zakaria, M. Yusof; Redza, M. Ridhwan; Sulaiman, M. Shahar; Tham, Ghalib; Abas, Sunhaji K.

2013-01-01

This paper presents an investigation of the welding sequence effect on induced angular distortion using FEM and experiments. The specimen of a combined joint geometry was modeled and simulated using Multipass Welding Advisor (MWA) in SYSWELD 2010 based on the thermal-elastic-plastic approach with low manganese carbon steel S3355J2G3 as specimen material and Goldak's double ellipsoid as heat source model. To validate the simulation results, a series of experiments was conducted with two different welding sequences using automated welding process, low carbon steel as parent metal, digital GMAW power source with premixed shielding gas and both-sided clamping technique. Based on the results, it was established that the thermo-elastic-plastic 3D FEM analysis shows good agreement with experimental results and the welding sequence “from outside to inside” induced less angular distortion compared to “from inside to outside”. -- Highlights: • 3D FEM was used to analyze the welding distortion on two different sequences. • Simulation results were validated with experiments using automated welding system. • Simulation results and experiments showed acceptable accuracy. • Welding sequence “outside–inside” showed less distortion than “inside–outside”

Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison

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Saville Barry J

2007-09-01

Full Text Available Abstract Background Ustilago maydis is the basidiomycete fungus responsible for common smut of corn and is a model organism for the study of fungal phytopathogenesis. To aid in the annotation of the genome sequence of this organism, several expressed sequence tag (EST libraries were generated from a variety of U. maydis cell types. In addition to utility in the context of gene identification and structure annotation, the ESTs were analyzed to identify differentially abundant transcripts and to detect evidence of alternative splicing and anti-sense transcription. Results Four cDNA libraries were constructed using RNA isolated from U. maydis diploid teliospores (U. maydis strains 518 × 521 and haploid cells of strain 521 grown under nutrient rich, carbon starved, and nitrogen starved conditions. Using the genome sequence as a scaffold, the 15,901 ESTs were assembled into 6,101 contiguous expressed sequences (contigs; among these, 5,482 corresponded to predicted genes in the MUMDB (MIPS Ustilago maydis database, while 619 aligned to regions of the genome not yet designated as genes in MUMDB. A comparison of EST abundance identified numerous genes that may be regulated in a cell type or starvation-specific manner. The transcriptional response to nitrogen starvation was assessed using RT-qPCR. The results of this suggest that there may be cross-talk between the nitrogen and carbon signalling pathways in U. maydis. Bioinformatic analysis identified numerous examples of alternative splicing and anti-sense transcription. While intron retention was the predominant form of alternative splicing in U. maydis, other varieties were also evident (e.g. exon skipping. Selected instances of both alternative splicing and anti-sense transcription were independently confirmed using RT-PCR. Conclusion Through this work: 1 substantial sequence information has been provided for U. maydis genome annotation; 2 new genes were identified through the discovery of 619

Cyclic Sequences, Events and Evolution of the Sino-Korean Plate,with a Discussion on the Evolution of Molar-tooth Carbonates,Phosphorites and Source Rocks

Institute of Scientific and Technical Information of China (English)

MENG Xianghua; GE Ming

2003-01-01

This paper gives an account of the research that the authors conducted on the cyclic sequences, events and evolutionary history from Proterozoic to Meso-Cenozoic in the Sino-Korean plate based on the principle of the Cosmos-Earth System. The authors divided this plate into 20 super-cyclic or super-mega-cyclic periods and more than 100 Oort periods. The research focused on important sea flooding events, uplift interruption events, tilting movement events, molar-tooth carbonate events, thermal events, polarity reversal events, karst events, volcanic explosion events and storm events, as well as types of resource areas and paleotectonic evolution. By means of the isochronous theory of the Cosmos-Earth System periodicity and based on long-excentricity and periodicity, the authors elaborately studied the paleogeographic evolution of the aulacogen of the Sino-Korean plate, the oolitic beach platform formation, the development of foreland basin and continental rift valley basin, and reconstructed the evolution of tectonic paleogeography and stratigraphic framework in the Sino-Korean plate in terms of evolutionary maps. Finally, the authors gave a profound discussion on the formation and development of molar-tooth carbonates, phosphorites and source rocks.

Proteomic analysis of carbon concentrating chemolithotrophic bacteria Serratia sp. for sequestration of carbon dioxide.

Science.gov (United States)

Bharti, Randhir K; Srivastava, Shaili; Thakur, Indu Shekhar

2014-01-01

A chemolithotrophic bacterium enriched in the chemostat in presence of sodium bicarbonate as sole carbon source was identified as Serratia sp. by 16S rRNA sequencing. Carbon dioxide sequestering capacity of bacterium was detected by carbonic anhydrase enzyme and ribulose-1, 5- bisphosphate carboxylase/oxygenase (RuBisCO). The purified carbonic anhydrase showed molecular weight of 29 kDa. Molecular weight of RuBisCO was 550 kDa as determined by fast protein liquid chromatography (FPLC), however, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) showed presence of two subunits whose molecular weights were 56 and 14 kDa. The Western blot analysis of the crude protein and purified sample cross reacted with RuBisCO large-subunit polypeptides antibodies showed strong band pattern at molecular weight around 56 kDa regions. Whole cell soluble proteins of Serratia sp. grown under autotrophic and heterotrophic conditions were resolved by two-dimensional gel electrophoresis and MALDI-TOF/MS for differential expression of proteins. In proteomic analysis of 63 protein spots, 48 spots were significantly up-regulated in the autotrophically grown cells; seven enzymes showed its utilization in autotrophic carbon fixation pathways and other metabolic activities of bacterium including lipid metabolisms indicated sequestration potency of carbon dioxide and production of biomaterials.

Proteomic analysis of carbon concentrating chemolithotrophic bacteria Serratia sp. for sequestration of carbon dioxide.

Directory of Open Access Journals (Sweden)

Randhir K Bharti

Full Text Available A chemolithotrophic bacterium enriched in the chemostat in presence of sodium bicarbonate as sole carbon source was identified as Serratia sp. by 16S rRNA sequencing. Carbon dioxide sequestering capacity of bacterium was detected by carbonic anhydrase enzyme and ribulose-1, 5- bisphosphate carboxylase/oxygenase (RuBisCO. The purified carbonic anhydrase showed molecular weight of 29 kDa. Molecular weight of RuBisCO was 550 kDa as determined by fast protein liquid chromatography (FPLC, however, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE showed presence of two subunits whose molecular weights were 56 and 14 kDa. The Western blot analysis of the crude protein and purified sample cross reacted with RuBisCO large-subunit polypeptides antibodies showed strong band pattern at molecular weight around 56 kDa regions. Whole cell soluble proteins of Serratia sp. grown under autotrophic and heterotrophic conditions were resolved by two-dimensional gel electrophoresis and MALDI-TOF/MS for differential expression of proteins. In proteomic analysis of 63 protein spots, 48 spots were significantly up-regulated in the autotrophically grown cells; seven enzymes showed its utilization in autotrophic carbon fixation pathways and other metabolic activities of bacterium including lipid metabolisms indicated sequestration potency of carbon dioxide and production of biomaterials.

Extension of the Si:C Stressor Thickness by Using Multiple ClusterCarbon Species

International Nuclear Information System (INIS)

Sekar, Karuppanan; Krull, Wade

2011-01-01

ClusterCarbon implantation is now well established as an attractive alternative for producing stress in advanced NMOS devices. ClusterCarbon has the advantage over monomer carbon implant in it's self-amorphization feature, eliminating the need for PAI implantation while producing highly substitutional carbon incorporation. To date, the limitation of this approach has been the high energy limit, due to the extraction limit of the available production tools for the preferred carbon species, which has been the C7Hx molecule. It is noted that the C7 species is produced by the breakup of the parent C14H14 molecule in the ion source. It is further noted that the preferred method of producing the Si:C stress layer is a multiple implant sequence with ClusterCarbon implants at various energies and doses designed to produce a carbon profile which is constant in-depth. The stressor thickness limit using C7 is known to be about 40 nm, which is less than the stressor thickness used in the conventional SiGe process for PMOS. In this work, it is shown that utilizing the C5 molecule which is also available from the breakup of C14H14 enables the stressor layer thickness to be extended to at least 60 nm, which is consistent with the conventional SiGe process. It will be shown that one additional C5 implant, performed after a standard C7 multiple implant sequence, can produce the extension of the stressor thickness while maintaining the flat depth profile. A detailed process characterization will be shown for this new process sequence.

Characterization of dissolved organic matter during landfill leachate treatment by sequencing batch reactor, aeration corrosive cell-Fenton, and granular activated carbon in series

International Nuclear Information System (INIS)

Bu Lin; Wang Kun; Zhao Qingliang; Wei Liangliang; Zhang Jing; Yang Junchen

2010-01-01

Landfill leachate is generally characterized as a complex recalcitrant wastewater containing high concentration of dissolved organic matter (DOM). A combination of sequencing batch reactor (SBR) + aeration corrosive cell-Fenton (ACF) + granular activated carbon (GAC) adsorption in series was proposed for the purpose of removing pollutants in the leachate. Fractionation was also performed to investigate the composition changes and characteristics of the leachate DOM in each treatment process. Experimental results showed that organic matter, in terms of chemical oxygen demand (COD), 5-day biological oxygen demand (BOD 5 ), and dissolved organic carbon (DOC), was reduced by 97.2%, 99.1%, and 98.7%, respectively. To differentiate the DOM portions, leachates were separated into five fractions by XAD-8 and XAD-4 resins: hydrophobic acid (HPO-A), hydrophobic neutral (HPO-N), transphilic acid (TPI-A), transphilic neutral (TPI-N), and hydrophilic fraction (HPI). The predominant fraction in the raw leachate was HPO-A (36% of DOC), while the dominant fraction in the final effluent was HPI (53% of DOC). Accordingly, macromolecules were degraded to simpler ones in a relatively narrow range below 1000 Da. Spectral and chromatographic analyses also showed that most humic-like substances in all fractions were effectively removed during the treatments and led to a simultaneous decrease in aromaticity.

Characterization of dissolved organic matter during landfill leachate treatment by sequencing batch reactor, aeration corrosive cell-Fenton, and granular activated carbon in series

Energy Technology Data Exchange (ETDEWEB)

Bu Lin [School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); Wang Kun [State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), Harbin Institute of Technology, Harbin 150090 (China); School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); Zhao Qingliang, E-mail: zhql1962@yahoo.com.cn [State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), Harbin Institute of Technology, Harbin 150090 (China); School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); Wei Liangliang; Zhang Jing; Yang Junchen [School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China)

2010-07-15

Landfill leachate is generally characterized as a complex recalcitrant wastewater containing high concentration of dissolved organic matter (DOM). A combination of sequencing batch reactor (SBR) + aeration corrosive cell-Fenton (ACF) + granular activated carbon (GAC) adsorption in series was proposed for the purpose of removing pollutants in the leachate. Fractionation was also performed to investigate the composition changes and characteristics of the leachate DOM in each treatment process. Experimental results showed that organic matter, in terms of chemical oxygen demand (COD), 5-day biological oxygen demand (BOD{sub 5}), and dissolved organic carbon (DOC), was reduced by 97.2%, 99.1%, and 98.7%, respectively. To differentiate the DOM portions, leachates were separated into five fractions by XAD-8 and XAD-4 resins: hydrophobic acid (HPO-A), hydrophobic neutral (HPO-N), transphilic acid (TPI-A), transphilic neutral (TPI-N), and hydrophilic fraction (HPI). The predominant fraction in the raw leachate was HPO-A (36% of DOC), while the dominant fraction in the final effluent was HPI (53% of DOC). Accordingly, macromolecules were degraded to simpler ones in a relatively narrow range below 1000 Da. Spectral and chromatographic analyses also showed that most humic-like substances in all fractions were effectively removed during the treatments and led to a simultaneous decrease in aromaticity.

Low-weight Impact Behaviour of Carbon Fibre Reinforced Methyl Methacrylate Nanocomposites

Directory of Open Access Journals (Sweden)

Virginija Jankauskaitė

2015-06-01

Full Text Available Inthis study, the carbon fibre reinforced methyl methacrylate (CF/MMA compositetoecap for safety shoes was manufactured to increase the energy absorptioncapacity during impact. Different types of nanofillers such as organic andinorganic nanotubes, unmodified and organically modified nanoclays were appliedto modify matrix impact properties. The drop-weight impact tests of thenanocomposite toecap were performed with respect to nanofiller nature andcarbon fibre stacking sequence. It was found that the most influence on thestiffness and impact damage of the carbon fibre methyl methacrylatenanocomposite toecaps besides stacking sequence show organic and inorganic nanotubesor unmodified nanoclay.DOI: http://dx.doi.org/10.5755/j01.ms.21.2.7075

Magnetostratigraphy of the impact breccias and post-impact carbonates from borehole Yaxcopoil-1, Chicxulub impact crater, Yucatán, Mexico

Science.gov (United States)

Rebolledo-Vieyra, Mario; Urrutia-Fucugauchi, Jaime

2004-06-01

We report the magnetostratigraphy of the sedimentary sequence between the impact breccias and the post-impact carbonate sequence conducted on samples recovered by Yaxcopoil-1 (Yax-1). Samples of impact breccias show reverse polarities that span up to ~56 cm into the postimpact carbonate lithologies. We correlate these breccias to those of PEMEX boreholes Yucatán-6 and Chicxulub-1, from which we tied our magnetostratigraphy to the radiometric age from a melt sample from the Yucatán-6 borehole. Thin section analyses of the carbonate samples showed a significant amount of dark minerals and glass shards that we identified as the magnetic carriers; therefore, we propose that the mechanism of magnetic acquisition within the carbonate rocks for the interval studied is detrital remanent magnetism (DRM). With these samples, we constructed the scale of geomagnetic polarities where we find two polarities within the sequence, a reverse polarity event within the impact breccias and the base of the post-impact carbonate sequence (up to 794.07 m), and a normal polarity event in the last ~20 cm of the interval studied. The polarities recorded in the sequence analyzed are interpreted to span from chron 29r to 29n, and we propose that the reverse polarity event lies within the 29r chron. The magnetostratigraphy of the sequence studied shows that the horizon at 794.11 m deep, interpreted as the K/T boundary, lies within the geomagnetic chron 29r, which contains the K/T boundary.

Ions in carbon dioxide at an atmospheric pressure

International Nuclear Information System (INIS)

Ikezoe, Yasumasa; Onuki, Kaoru; Shimizu, Saburo; Nakajima, Hayato; Sato, Shoichi; Matsuoka, Shingo; Nakamura, Hirone; Tamura, Takaaki

1985-01-01

The formation and the subsequent reactions of positive and negative ions were observed by a time resolved atmospheric pressure ionization mass spectrometer (TRAPI) in an atmospheric pressure carbon dioxide added with small amounts of carbon monoxide and oxygen. A relatively stable ion of (44 x n) + (n >= 2) having a different reactivity from that of (CO 2 ) + sub(n) was found to be one of major ionic species in this gas system. This species was tentatively assigned as [O 2 (CO) 2 ] + (CO 2 )sub(n-2). A new reaction sequence of positive ions is proposed which can be operative in the radiolysis of carbon dioxide at 1 atm. (author)

Specificity of mutations induced by carbon ions in budding yeast Saccharomyces cerevisiae

International Nuclear Information System (INIS)

Matuo, Youichirou; Nishijima, Shigehiro; Hase, Yoshihiro; Sakamoto, Ayako; Tanaka, Atsushi; Shimizu, Kikuo

2006-01-01

To investigate the nature of mutations induced by accelerated ions in eukaryotic cells, the effects of carbon-ion irradiation were compared with those of γ-ray irradiation in the budding yeast Saccharomyces cerevisiae. The mutational effect and specificity of carbon-ion beams were studied in the URA3 gene of the yeast. Our experiments showed that the carbon ions generated more than 10 times the number of mutations induced by γ-rays, and that the types of base changes induced by carbon ions include transversions (68.7%), transitions (13.7%) and deletions/insertions (17.6%). The transversions were mainly G:C → T:A, and all the transitions were G:C → A:T. In comparison with the surrounding sequence context of mutational base sites, the C residues in the 5'-AC(A/T)-3' sequence were found to be easily changed. Large deletions and duplications were not observed, whereas ion-induced mutations in Arabidopsis thaliana were mainly short deletions and rearrangements. The remarkable feature of yeast mutations induced by carbon ions was that the mutation sites were localized near the linker regions of nucleosomes, whereas mutations induced by γ-ray irradiation were located uniformly throughout the gene

Cyclic Cratonic Carbonates and Phanerozoic Calcite Seas.

Science.gov (United States)

Wilkinson, Bruce H.

1982-01-01

Discusses causes of cyclicity in cratonic carbonate sequences and evidence for and potential significance of postulated primary calcite sediment components in past Paleozoic seas, outlining problems, focusing on models explaining existing data, and identifying background. Future sedimentary geologists will need to address these and related areas…

Cloning and expression of gamma carbonic anhydrase from Serratia sp. ISTD04 for sequestration of carbon dioxide and formation of calcite.

Science.gov (United States)

Srivastava, Shaili; Bharti, Randhir Kumar; Verma, Praveen Kumar; Thakur, Indu Shekhar

2015-01-01

Bacterial strains isolated from marble mines rock and enriched in the chemostat culture with different concentrations of sodium bicarbonate. The enriched consortium had six bacterial isolates. One of bacterium isolate showed carbonic anhydrase (CA) activity by catalyzing the reversible hydration reaction of carbon dioxide to bicarbonate. The bacterium was identified as Serratia sp. by 16S rRNA sequence analysis. The carbonic anhydrase gene from Serratia sp. was found to be homologous with gamma carbonic anhydrase. The carbonic anhydrase gene was cloned in PET21b(+) and expressed it in recombinant Escherichia coli BL21 (DE3) with His-tag at the C-terminus. The recombinant protein was purified efficiently by using one-step nickel affinity chromatography. Expected size of carbonic anhydrase was approximately 29 kDa in SDS-PAGE gel. Recombinant carbonic anhydrase enzyme was used for biomineralization-based conversion of atmospheric CO2 into valuable calcite minerals. The calcification was confirmed by using XRD, FTIR, EDX and SEM analysis. Copyright © 2015 Elsevier Ltd. All rights reserved.

CRL 2688: A post-carbon-star object and probable planetary nebula progenitor

International Nuclear Information System (INIS)

Zuckerman, B.; Gilra, D.P.; Turner, B.E.; Morris, M.; Palmer, P.

1976-01-01

Millimeter-wavelength emission is observed toward CRL 2688 from H 12 CN, H 13 CN, CS, and HC 3 N. The similarity of this emission and that from the molecular envelope of the carbon star IRC+10216 establishes, beyond a reasonable doubt, that CRL 2688 is a post--carbon-star object. It appears probable that both of these objects will evolve into planetary nebulae. An evolutionary sequence leading from carbon stars to planetary nebulae is outlined

The palaeoenvironmental implications of carbonate petrography, kerogen distribution and carbon and oxygen isotope variations in the early Proterozoic transition from Campbellrand limestone to Kuruman iron-formation deposition in Griqualand West

International Nuclear Information System (INIS)

Beukes, N.J.; Klein, C.; Kaufman, A.J.; Hayes, J.M.

1990-01-01

The Griqualand West area of the Transvaal basin in South Africa offers a unique opportunity to study the relationships between the deposition of limestone and iron-formation. The stratigraphic sequence includes the transition from microbialaminated Campbellrand carbonates to the conformably Kuruman iron formation composed mainly of microbanded iron-formation. The relationships between carbonate mineral paragenesis, kerogen abundance, and isotopic compositions of carbon and oxygen for the same drill core samples are reported. The significance of whole rock carbon-isotopic compositions of iron-formations relative to those of limestones and dolomites are explored. 6 refs

Draft Genome Sequence of Methylocella silvestris TVC, a Facultative Methanotroph Isolated from Permafrost

OpenAIRE

Wang, Jing; Geng, Kan; Farhan Ul Haque, Muhammad; Crombie, Andrew; Street, Lorna E.; Wookey, Philip A.; Ma, Ke; Murrell, J. Colin; Pratscher, Jennifer

2018-01-01

Permafrost environments play a crucial role in global carbon and methane cycling. We report here the draft genome sequence of Methylocella silvestris TVC, a new facultative methanotroph strain, isolated from the Siksik Creek catchment in the continuous permafrost zone of Inuvik (Northwest Territories, Canada).

Rates of carbonate soil evolution from carbon, U- and Th-series isotope studies: Example of the Astian sands (SE France)

Science.gov (United States)

Barbecot, Florent; Ghaleb, Bassam; Hillaire-Marcel, Claude

2015-04-01

In carbonate rich soils, C-isotopes (14C, 13C) and carbonate mass budget may inform on centennial to millennial time scale dissolution/precipitation processes and weathering rates, whereas disequilibria between in the U- and Th-decay series provide tools to document high- (228Ra-228Th-210Pb) to low- (234U, 230Th, 231Pa, 226Ra) geochemical processes rate, covering annual to ~ 1Ma time scales, governing both carbonate and silicate soil fractions. Because lithology constitutes a boundary condition, we intend to illustrate the behavior of such isotopes in soils developed over Astian sands formation (up to ~ 30% carbonate) from the Béziers area (SE France). A >20 m thick unsaturated zone was sampled firstly along a naturally exposed section, then in a cored sequence. Geochemical and mineralogical analyses, including stable isotopes and 14C-measurements, were complemented with 228U, 234U, 230Th, 226Ra, 210Pb and 228Th, 232Th measurements. Whereas the upper 7 m depict geochemical and isotopic features forced by dissolution/precipitation processes leading to variable radioactive disequilibria, but overall deficits in more soluble elements of the decay series, the lower part of the sequence shows strong excesses in 234U and 230Th over parent isotopes (i.e., 238U and 234U, respectively). These features might have been interpreted as the result of successive phases of U-loss and gains. However, 226Ra and 230Th are in near-equilibrium, thus leading to conclude at a more likely slow enrichment process in both 234Th(234U) and 230Th, which we link to dissolved U-decay during groundwater recharge events. In addition, 210Pb deficits (vs parent 226Ra) are observed down to 12 m along the natural outcropping section and below the top-soil 210Pb-excess in the cored sequence, due to gaseous 222Rn-diffusion over the cliff outcrop. Based on C-isotope and chemical analysis, reaction rates at 14C-time scale are distinct from those estimates at the short- or long-lived U-series isotopes

Successful treatment of high azo dye concentration wastewater using combined anaerobic/aerobic granular activated carbon-sequencing batch biofilm reactor (GAC-SBBR): simultaneous adsorption and biodegradation processes.

Science.gov (United States)

Hosseini Koupaie, E; Alavi Moghaddam, M R; Hashemi, S H

2013-01-01

The application of a granular activated carbon-sequencing batch biofilm reactor (GAC-SBBR) for treatment of wastewater containing 1,000 mg/L Acid Red 18 (AR18) was investigated in this research. The treatment system consisted of a sequencing batch reactor equipped with moving GAC as biofilm support. Each treatment cycle consisted of two successive anaerobic (14 h) and aerobic (8 h) reaction phases. Removal of more than 91% chemical oxygen demand (COD) and 97% AR18 was achieved in this study. Investigation of dye decolorization kinetics showed that the dye removal was stimulated by the adsorption capacity of the GAC at the beginning of the anaerobic phase and then progressed following a first-order reaction. Based on COD analysis results, at least 77.8% of the dye total metabolites were mineralized during the applied treatment system. High-performance liquid chromatography analysis revealed that more than 97% of 1-naphthyalamine-4-sulfonate as one of the main sulfonated aromatic constituents of AR18 was removed during the aerobic reaction phase. According to the scanning electron microscopic analysis, the microbial biofilms grew in most cavities and pores of the GAC, but not on the external surfaces of the GAC.

Depositional History and Sequence Stratigraphy of the Middle Ordovician Yeongheung Formation (Yeongweol Group), Taebaeksan Basin, mid-east Korea

Science.gov (United States)

Kwon, Yoo Jin; Kwon, Yi Kyun

2017-04-01

The Middle Ordovician Yeongheung Formation consists of numerous meter-scale, shallowing-upward cycles which were deposited on a shallow-marine carbonate platform. Many diagnostic sedimentary textures and structures such as supratidal laminite, tepee structure, and solution-collapsed breccia are observed, which enable to infer the dry climate and high salinity conditions during deposition of the formation. In order to understand its depositional history, this study focuses on vertical and spatial stacking patterns of the second- to third-order sequences through the detailed outcrop description and geologic mapping. A total 19 lithofacies have been recognized, which can be grouped into 5 facies associations (FAs): FA1 (Supratidal flat), FA2 (Supratidal or dolomitization of peritidal facies), FA3 (Intertidal flat), FA4 (Shallow subtidal to peritidal platform), FA5 (Shallow subtidal shoal). Global mega-sequence boundary (Sauk-Tippecanoe) occurs in solution-collapsed breccia zone in the lower part of the formation. Correlation of the shallowing-upward cycle stacking pattern across the study area defines 6 transgressive-regressive depositional sequences. Each depositional sequences comprises a package of vertical and spatial staking of shallow subtidal cycles in the lower part and peritidal cycles in the upper part of the formation. According to sequence stratigraphic interpretation, the reconstructed relative sea-level curve of the Yeongweol platform is very similar to that of the Taebaek platform. Based on the absence of siliciclastic sequence such as the Jigunsan Formation and the lithologic & stratigraphic differences, however, the Yeongweol and Taebaek groups might not belong to a single depositional system within the North China platform. The Yeongweol Group can be divided by the four subunits into their unique lithologic successions and geographic distributions. The Eastern subunit of the Yeongweol Group is composed dominantly of carbonate rocks with a high

Specificity of mutations induced by carbon ions in budding yeast Saccharomyces cerevisiae

Energy Technology Data Exchange (ETDEWEB)

Matuo, Youichirou [Graduate School of Engineering, Osaka University, Yamada-oka 2-1, Suita, Osaka 565-0871 (Japan); Nishijima, Shigehiro [Graduate School of Engineering, Osaka University, Yamada-oka 2-1, Suita, Osaka 565-0871 (Japan); Hase, Yoshihiro [Radiation-Applied Biology Division, Quantum Beam Science Directorate, Japan Atomic Energy Agency (JAEA), Watanuki-machi 1233, Takasaki, Gunma 370-1292 (Japan); Sakamoto, Ayako [Radiation-Applied Biology Division, Quantum Beam Science Directorate, Japan Atomic Energy Agency (JAEA), Watanuki-machi 1233, Takasaki, Gunma 370-1292 (Japan); Tanaka, Atsushi [Radiation-Applied Biology Division, Quantum Beam Science Directorate, Japan Atomic Energy Agency (JAEA), Watanuki-machi 1233, Takasaki, Gunma 370-1292 (Japan); Shimizu, Kikuo [Radioisotope Research Center, Osaka University, Yamada-oka 2-4, Suita, Osaka 565-0871 (Japan)]. E-mail: shimizu@rirc.osaka-u.ac.jp

2006-12-01

To investigate the nature of mutations induced by accelerated ions in eukaryotic cells, the effects of carbon-ion irradiation were compared with those of {gamma}-ray irradiation in the budding yeast Saccharomyces cerevisiae. The mutational effect and specificity of carbon-ion beams were studied in the URA3 gene of the yeast. Our experiments showed that the carbon ions generated more than 10 times the number of mutations induced by {gamma}-rays, and that the types of base changes induced by carbon ions include transversions (68.7%), transitions (13.7%) and deletions/insertions (17.6%). The transversions were mainly G:C {sup {yields}} T:A, and all the transitions were G:C {sup {yields}} A:T. In comparison with the surrounding sequence context of mutational base sites, the C residues in the 5'-AC(A/T)-3' sequence were found to be easily changed. Large deletions and duplications were not observed, whereas ion-induced mutations in Arabidopsis thaliana were mainly short deletions and rearrangements. The remarkable feature of yeast mutations induced by carbon ions was that the mutation sites were localized near the linker regions of nucleosomes, whereas mutations induced by {gamma}-ray irradiation were located uniformly throughout the gene.

Lower Cretaceous paleo-Vertisols and sedimentary interrelationships in stacked alluvial sequences, Utah, USA

Science.gov (United States)

Joeckel, R. M.; Ludvigson, G. A.; Kirkland, J. I.

2017-11-01

The Yellow Cat Member of the Cedar Mountain Formation in Poison Strip, Utah, USA, consists of stacked, erosionally bounded alluvial sequences dominated by massive mudstones (lithofacies Fm) with paleo-Vertisols. Sediment bodies within these sequences grade vertically and laterally into each other at pedogenic boundaries, across which color, texture, and structures (sedimentary vs. pedogenic) change. Slickensides, unfilled (sealed) cracks, carbonate-filled cracks, and deeper cracks filled with sandstone; the latter features suggest thorough desiccation during aridification. Thin sandstones (Sms) in some sequences, typically as well as laminated to massive mudstones (Flm) with which they are interbedded in some cases, are interpreted as avulsion deposits. The termini of many beds of these lithofacies curve upward, parallel to nearby pedogenic slickensides, as the features we call ;turnups.; Turnups are overlain or surrounded by paleosols, but strata sheltered underneath beds with turnups retain primary sedimentary fabrics. Turnups were produced by movement along slickensides during pedogenesis, by differential compaction alongside pre-existing gilgai microhighs, or by a combination of both. Palustrine carbonates (lithofacies C) appear only in the highest or next-highest alluvial sequences, along with a deep paleo-Vertisol that exhibits partially preserved microrelief at the base of the overlying Poison Strip Member. The attributes of the Yellow Cat Member suggest comparatively low accommodation, slow accumulation, long hiatuses in clastic sedimentation, and substantial time intervals of subaerial exposure and pedogenesis; it appears to be distinct among the members of the Cedar Mountain Formation in these respects.

Sequence-Stratigraphic Analysis of the Regional Observation Monitoring Program (ROMP) 29A Test Corehole and Its Relation to Carbonate Porosity and Regional Transmissivity in the Floridan Aquifer System, Highlands County, Florida

Science.gov (United States)

Ward, W. C.; Cunningham, K.J.; Renken, R.A.; Wacker, M.A.; Carlson, J.I.

2003-01-01

An analysis was made to describe and interpret the lithology of a part of the Upper Floridan aquifer penetrated by the Regional Observation Monitoring Program (ROMP) 29A test corehole in Highlands County, Florida. This information was integrated into a one-dimensional hydrostratigraphic model that delineates candidate flow zones and confining units in the context of sequence stratigraphy. Results from this test corehole will serve as a starting point to build a robust three-dimensional sequence-stratigraphic framework of the Floridan aquifer system. The ROMP 29A test corehole penetrated the Avon Park Formation, Ocala Limestone, Suwannee Limestone, and Hawthorn Group of middle Eocene to Pliocene age. The part of the Avon Park Formation penetrated in the ROMP 29A test corehole contains two composite depositional sequences. A transgressive systems tract and a highstand systems tract were interpreted for the upper composite sequence; however, only a highstand systems tract was interpreted for the lower composite sequence of the deeper Avon Park stratigraphic section. The composite depositional sequences are composed of at least five high-frequency depositional sequences. These sequences contain high-frequency cycle sets that are an amalgamation of vertically stacked high-frequency cycles. Three types of high-frequency cycles have been identified in the Avon Park Formation: peritidal, shallow subtidal, and deeper subtidal high-frequency cycles. The vertical distribution of carbonate-rock diffuse flow zones within the Avon Park Formation is heterogeneous. Porous vuggy intervals are less than 10 feet, and most are much thinner. The volumetric arrangement of the diffuse flow zones shows that most occur in the highstand systems tract of the lower composite sequence of the Avon Park Formation as compared to the upper composite sequence, which contains both a backstepping transgressive systems tract and a prograding highstand systems tract. Although the porous and permeable

Microfacies, Depositional environment and Sequence Stratigraphy of Upper Carboniferous- Lower Permian rocks from Ozbak-Kuh region (Zaladou Section, East Central Iran

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Ali Ahmadi

2016-01-01

Full Text Available Zaladou section is located in Ozbak-Kuh mountains in the nourthen part of Tabas block and consist of shale, limy sandstone, limestone and dolomite. Continous relationship of Upper Carboniferous and Lower Permian deposits, is quite evident in Zaladou section. The lower boundry of this section is located on the Absheni formation of Sardar Group with disconformity surface, and upper boundry’s is covered by disconformity surface and bauxite horizon of Bagh-e-Vang formation. According to the lithological Characters and microscopic studies, tidal flat, lagoon, bar, tidal inlet and open marine sub-environment are identified for Zaladou section. Results of this study show that Zaladou section was deposited in silisiclastic-carbonate mix homoclinal ramp in late Carboniferous and in carbonate homoclinal ramp in early Permian. Field study, microfacies and analysis through the sequence led to recognition of main sequence surface, such as: sequence boundry, maximum flooding surface, marine flooding surface, system tracts and two depositional sequences.

Effect of carbon dioxide and bicarbonate as inorganic carbon sources on growth and adaptation of autohydrogenotrophic denitrifying bacteria

International Nuclear Information System (INIS)

Ghafari, Shahin; Hasan, Masitah; Aroua, Mohamed Kheireddine

2009-01-01

Acclimation of autohydrogenotrophic denitrifying bacteria using inorganic carbon source (CO 2 and bicarbonate) and hydrogen gas as electron donor was performed in this study. In this regard, activated sludge was used as the seed source and sequencing batch reactor (SBR) technique was applied for accomplishing the acclimatization. Three distinct strategies in feeding of carbon sources were applied: (I) continuous sparging of CO 2 , (II) bicarbonate plus continuous sparging of CO 2 , and (III) only bicarbonate. The pH-reducing nature of CO 2 showed an unfavorable impact on denitrification rate; however bicarbonate resulted in a buffered environment in the mixed liquor and provided a suitable mean to maintain the pH in the desirable range of 7-8.2. As a result, bicarbonate as the only carbon source showed a faster adaptation, while carbon dioxide as the only carbon source as well as a complementary carbon source added to bicarbonate resulted in longer acclimation period. Adapted hydrogenotrophic denitrifying bacteria, using bicarbonate and hydrogen gas in the aforementioned pH range, caused denitrification at a rate of 13.33 mg NO 3 - -N/g MLVSS/h for degrading 20 and 30 mg NO 3 - -N/L and 9.09 mg NO 3 - -N/g MLVSS/h for degrading 50 mg NO 3 - -N/L

Centennial-scale records of total organic carbon in sediment cores from the South Yellow Sea, China

Science.gov (United States)

Zhu, Qing; Lin, Jia; Hong, Yuehui; Yuan, Lirong; Liu, Jinzhong; Xu, Xiaoming; Wang, Jianghai

2018-01-01

Global carbon cycling is a significant factor that controls climate change. The centennial-scale variations in total organic carbon (TOC) contents and its sources in marginal sea sediments may reflect the influence of human activities on global climate change. In this study, two fine-grained sediment cores from the Yellow Sea Cold Water Mass of the South Yellow Sea were used to systematically determine TOC contents and stable carbon isotope ratios. These results were combined with previous data of black carbon and 210Pb dating from which we reconstructed the centennial-scale initial sequences of TOC, terrigenous TOC (TOCter) and marine autogenous TOC (TOCmar) after selecting suitable models to correct the measured TOC (TOCcor). These sequences showed that the TOCter decreased with time in the both cores while the TOCmar increased, particularly the rapid growth in core H43 since the late 1960s. According to the correlation between the Huanghe (Yellow) River discharge and the TOCcor, TOCter, or TOCmar, we found that the TOCter in the two cores mainly derived from the Huanghe River and was transported by it, and that higher Huanghe River discharge could strengthen the decomposition of TOCmar. The newly obtained initial TOC sequences provide important insights into the interaction between human activities and natural processes.

Composition and origin of Early Cambrian Tiantaishan phosphorite-Mn carbonate ores, Shaanxi Province, China

Science.gov (United States)

Hein, J.R.; Fan, D.; Ye, J.; Liu, T.; Yeh, H.-W.

1999-01-01

The Tiantaishan phosphorite-Mn carbonate ores occur in the Early Cambrian Tananpo Formation in complexly folded and faulted rocks located in southern Shaanxi Province. About 65 x 106 tonnes of 17% P2O5 ore reserves exist and Mn-ore reserves are about 8.3 x 106 tonnes of +18% Mn. The stratigraphic sequence in ascending order consists of black phyllite, black to gray phosphorite ore, black phyllite, rhodochrostone ore, Mn mixed-carbonates, and dolostone. Data are presented from microprobe mineral chemistry, whole-rock chemistry, stable isotopes of carbonates, X-ray mineralogy, petrographic and SEM observations, and statistical analysis of chemical data. The dominant ore-forming minerals are hydroxy- and carbonate fluorapatite and Ca rhodochrosite, with Mg kutnahorite and dolomite comprising the Mn mixed-carbonate section. Pyrite occurs in all rock types and alabandite (MnS) occurs throughout the rhodochrostone section. The mean P2O5 content of phosphorite is 31% and argillaceous phosphorite is 16%, while the mean MnO content of rhodochrostone ore is 37%. Phosphorite ores are massive, spheroidal, laminated, and banded, while rhodochrostone ores have oolitic, spheroidal, and granular fabrics. The most distinguishing characteristics of the ores are high total organic carbon (TOC) contents (mean 8.4%) in the phosphorite and high P2O5 contents (mean 2.7%) in the rhodochrostone ore. The atypically high TOC contents in the Tiantaishan phosphorite probably result from very strong productivity leading to high sedimentation rates accompanied by weak reworking of sediments; poor utilization of the organic matter by bacteria; and/or partial replacement of bacterial or algal mats by the apatite. The depositional setting of the ores was the margin of an epicontinental seaway created as a direct consequence of global processes that included break-up of a supercontinent, formation of narrow seaways, creation of extensive continental shelves, overturn of stagnant, metal-rich deep

Facies-succession and architecture of the third-order sequences and their stratigraphic framework of the Devonian in Yunnan-Guizhou-Guangxi area, South China

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Mei Mingxiang

2013-01-01

Full Text Available The Caledonian orogeny at the end of the Silurian resulted in great changes in the palaeogeography in the Yunnan-Guizhou-Guangxi area of South China; the continental area of the Early Paleozoic evolved into the extensive Dian-Qian-Gui Sea in the Late Paleozoic. Early in the Devonian, as a result of a major transgression, seawater encroached gradually from the south to the north and clastic facies were deposited. Carbonate deposition was then established in the Yunnan-Guizhou-Guangxi area, with a palaeogeography marked by attached platforms, isolated platforms and narrow basins. As a result of the Ziyun movement towards the end of the Devonian, the Upper Devonian strata are regressive and thin out from the open-sea to the land areas. A study of the nature and distribution of sedimentary facies in space and time recognises 13 third-order sequences in the Devonian strata in Yunnan-Guizhou-Guangxi area, and these form two second-order sequences. The strata of the Lower Devonian comprise 5 third-order sequences (SQ1 to SQ5, which are dominated by transgressive clastics. 4 third-order sequences (SQ6 to SQ9 in the Middle Devonian are characterized by alternations of transgressive clastics and highstand carbonates. In the Upper Devonian, carbonates constitute 4 third-order sequences (SQ10 to SQ13, which are generally marked by the transgressive limestones and highstand dolomites. On the basis of earlier biostratigraphic studies, sea-level changes represented by the third-order sequences with their different facies successions are explored, and the sequence stratigraphic framework is established. Therefore, the Devonian strata in the study area provide an example for further understanding of depositional trends within the sequence-stratigraphic framework.

Investigating Interactions between the Silica and Carbon Cycles during Precipitation and Early Diagenesis of Authigenic Clay/Carbonate-Mineral Associations in the Carbonate Rock Record

Science.gov (United States)

McKenzie, J. A.; Francisca Martinez Ruiz, F.; Sanchez-Roman, M.; Anjos, S.; Bontognali, T. R. R.; Nascimento, G. S.; Vasconcelos, C.

2017-12-01

The study of authigenic clay/carbonate-mineral associations within carbonate sequences has important implications for the interpretation of scientific problems related with rock reservoir properties, such as alteration of potential porosity and permeability. More specifically, when clay minerals are randomly distributed within the carbonate matrix, it becomes difficult to predict reservoir characteristics. In order to understand this mineral association in the geological record, we have undertaken a comparative study of specially designed laboratory experiments with modern environments, where clay minerals have been shown to precipitate together with a range of carbonate minerals, including calcite, Mg-calcite and dolomite. Two modern dolomite-forming environments, the Coorong lakes, South Australia and Brejo do Espinho Rio de Janeiro, Brazil, were selected for this investigation. For comparative evaluation, enrichment microbial culture experiments, using natural pore water from Brejo do Espinho as the growth medium to promote mineral precipitation, were performed under both aerobic and anaerobic conditions. To establish the environmental parameters and biological processes facilitating the dual mineral association, the experimental samples have been compared with the natural minerals using HRTEM measurements. The results demonstrate that the clay and carbonate minerals apparently do not co-precipitate, but the precipitation of the different minerals in the same sample has probably occurred under different environmental conditions with variable chemistries, e.g., hypersalinity versus normal salinity resulting from the changing ratio of evaporation versus precipitation. Thus, the investigated mineral association is not a product of diagenetic processes but of sequential in situ precipitation processes related to changes in the silica and carbon availability. Implications for ancient carbonate formations will be presented and discussed in the context of a specific

Draft Genome Sequence of Methylocella silvestris TVC, a Facultative Methanotroph Isolated from Permafrost.

Science.gov (United States)

Wang, Jing; Geng, Kan; Farhan Ul Haque, Muhammad; Crombie, Andrew; Street, Lorna E; Wookey, Philip A; Ma, Ke; Murrell, J Colin; Pratscher, Jennifer

2018-02-22

Permafrost environments play a crucial role in global carbon and methane cycling. We report here the draft genome sequence of Methylocella silvestris TVC, a new facultative methanotroph strain, isolated from the Siksik Creek catchment in the continuous permafrost zone of Inuvik (Northwest Territories, Canada). Copyright © 2018 Wang et al.

Oxidation kinetics of a continuous carbon phase in a nonreactive matrix

Science.gov (United States)

Eckel, Andrew J.; Cawley, James D.; Parthasarathy, Triplicane A.

1995-01-01

Analytical solutions of and experimental results on the oxidation kinetics of carbon in a pore are presented. Reaction rate, reaction sequence, oxidant partial pressure, total system pressure, pore/crack dimensions, and temperature are analyzed with respect to the influence of each on an overall linear-parabolic rate relationship. Direct measurement of carbon recession is performed using two microcomposite model systems oxidized in the temperature range of 700 to 1200 C, and for times to 35 h. Experimental results are evaluated using the derived analytical solutions. Implications on the oxidation resistance of continuous-fiber-reinforced ceramic-matrix composites containing a carbon constituent are discussed.

Citrus plastid-related gene profiling based on expressed sequence tag analyses

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Tercilio Calsa Jr.

2007-01-01

Full Text Available Plastid-related sequences, derived from putative nuclear or plastome genes, were searched in a large collection of expressed sequence tags (ESTs and genomic sequences from the Citrus Biotechnology initiative in Brazil. The identified putative Citrus chloroplast gene sequences were compared to those from Arabidopsis, Eucalyptus and Pinus. Differential expression profiling for plastid-directed nuclear-encoded proteins and photosynthesis-related gene expression variation between Citrus sinensis and Citrus reticulata, when inoculated or not with Xylella fastidiosa, were also analyzed. Presumed Citrus plastome regions were more similar to Eucalyptus. Some putative genes appeared to be preferentially expressed in vegetative tissues (leaves and bark or in reproductive organs (flowers and fruits. Genes preferentially expressed in fruit and flower may be associated with hypothetical physiological functions. Expression pattern clustering analysis suggested that photosynthesis- and carbon fixation-related genes appeared to be up- or down-regulated in a resistant or susceptible Citrus species after Xylella inoculation in comparison to non-infected controls, generating novel information which may be helpful to develop novel genetic manipulation strategies to control Citrus variegated chlorosis (CVC.

Stable isotope composition of bulk and secondary carbonates from the Quaternary loess-paleosol sequence in Sutto, Hungary

DEFF Research Database (Denmark)

Koeniger, Paul; Barta, Gabriella; Thiel, Christine

2014-01-01

reveal pedogenetic information during the different climatic phases. Carbon and oxygen isotope analyses are valuable to classify secondary carbonates and to serve as proxies for the interpretation of paleoenvironmental conditions, e.g. moisture conditions, leaching, the role of organic matter...

Oxidation mechanism and passive behaviour of nickel in molten carbonate

Energy Technology Data Exchange (ETDEWEB)

Vossen, J.P.T. (ECN Fossil Fuels, Petten (Netherlands)); Ament, P.C.H.; De Wit, J.H.W. (Div. of Corrosion, Lab. for Maaterials Sceince, Delft Univ. of Technology, Delft (Netherlands))

1994-07-01

The oxidation and passivation mechanism and the passive behaviour of nickel in molten carbonate have been investigated with impedance measurements. The oxidation of nickel proceeds according to a dissolution and reprecipitation process. The slowest steps in the reaction sequence are the dissociation reaction of the carbonate and the diffusion of the formed NiO to the metal surface. In the passive range, dissolution of Ni[sup 2+] proceeds after diffusion of Ni[sup 2+] through the oxide layer. The Ni[sup 2+] is formed at the metal/oxide interface. The slowest process is the diffusion of bivalent nickel ions through the passive scale. The formation of trivalent nickel ions probably takes place at the oxide/melt interface. This reaction is accompanied by the incorporation of an oxygen ion and a nickel vacancy in the NiO lattice. The trivalent nickel ions and the nickel vacancy diffuse to the bulk of the oxide scale. The slowest step in this sequence is the dissociation of the carbonate ions and the incorporation of the oxygen ion in the NiO lattice. 9 figs., 2 tabs., 11 refs.

Facies analysis and paleoenvironmental reconstruction of Upper Cretaceous sequences in the eastern Para-Tethys Basin, NW Iran

Energy Technology Data Exchange (ETDEWEB)

Omidvar, M.; Safari, A.; Vaziri-Moghaddam, H.; Ghalavand, H.

2016-07-01

Upper Cretaceous mixed carbonate-siliciclastic sequences are among the most important targets for hydrocarbon exploration in the Moghan area, located in the eastern Para-Tethys Basin. Despite of their significance, little is known about their facies characteristics and depositional environments. Detailed facies analysis and paleoenvironmental reconstruction of these sequences have been carried out in eight surface sections. Accordingly, four siliciclastic facies, eight carbonate facies and one volcanic facies have been recognized. Detailed facies descriptions and interpretations, together with the results of facies frequency analysis, standard facies models and Upper Cretaceous depositional models of Para-Tethys Basin, have been integrated and a non-rimmed carbonate platform is presented. This platform was affected by siliciclastic influx, in the form of coastal fan delta and submarine fans in the shallow- to deep-marine parts, respectively. This model is interpreted to be shallower in the central and northeastern parts of the Moghan area. Toward the southeast and southwest, this shallow platform turns into deep marine settings along steep slopes without remarkable marginal barriers. (Author)

Diagenesis of lower Cretaceous pelagic carbonates, North Atlantic: Paleoceanographic signals obscured

Science.gov (United States)

Frank, T.D.; Arthur, M.A.; Dean, W.E.

1999-01-01

The stable isotope and minor element geochemistry of Neocomian (Lower Cretaceous) pelagic carbonates of the North Atlantic Basin (Deep Sea Drilling Project Sites 105, 367, 387, 391, and 603) was examined to develop a diagenetic model for pelagic limestones. In particular, we hoped to test the fidelity of whole-rock geochemical records as paleoceanographic indicators for pelagic deposits of pre-Aptian age, in which individual microfossils are not available for analysis. Data indicate that in addition to depth of burial, rhythmic variations in primary carbonate content have strongly controlled diagenetic patterns and associated geochemical signatures in these Neocomian sequences. Samples become increasingly depleted in Sr and 18O with increasing CaCO3 content. Within individual sedimentary sections, substantial decreases in Sr/Ca ratios and ??18O values are evident over a range of 4 to 98% CaCO3. However, even over a relatively narrow range of 50 to 98% CaCO3 a 2.5%c variation in ??18O values and a change of a factor of 1.7 in Sr/Ca ratios are observed. Carbon isotope compositions do not vary as extensively with CaCO3 content, but carbonate-rich intervals tend to be relatively depleted in 13C. Petrographic analysis reveals that these geochemical patterns are related to the transfer of CaCO3 from carbonate-poor intervals (calcareous shales and marlstones) to adjacent carbonate-rich intervals (limestones) during burial compaction and pressure solution. This process results in the addition of diagenetic cement to carbonate-rich intervals to produce a bulk composition that is relatively depleted in Sr and 18O and, at the same time, enables the retention of more-or-less primary carbonate that is relatively enriched in Sr and 18O in adjacent carbonate-poor intervals. Thus, although cyclic variations in CaCO3 content are primary in the Neocomian sequences examined, measured variations in Sr/Ca ratios and ??18O values are not and, as such, do not provide reliable proxies for

Nuclear fusion and carbon flashes on neutron stars

Science.gov (United States)

Taam, R. E.; Picklum, R. E.

1978-01-01

This paper reports on detailed calculations of the thermal evolution of the carbon-burning shells in the envelopes of accreting neutron stars for mass-accretion rates of 1 hundred-billionth to 2 billionths of a solar mass per yr and neutron-star masses of 0.56 and 1.41 solar masses. The work of Hansen and Van Horn (1975) is extended to higher densities, and a more detailed treatment of nuclear processing in the hydrogen- and helium-burning regions is included. Results of steady-state calculations are presented, and results of time-dependent computations are examined for accretion rates of 3 ten-billionths and 1 billionth of solar mass per yr. It is found that two evolutionary sequences lead to carbon flashes and that the carbon abundance at the base of the helium shell is a strong function of accretion rate. Upper limits are placed on the accretion rates at which carbon flashes will be important.

Draft genome sequence of Acidithiobacillus ferrooxidans YQH-1

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Lei Yan

2015-12-01

Full Text Available Acidithiobacillus ferrooxidans YQH-1 is a moderate acidophilic bacterium isolated from a river in a volcano of Northeast China. Here, we describe the draft genome of strain YQH-1, which was assembled into 123 contigs containing 3,111,222 bp with a G + C content of 58.63%. A large number of genes related to carbon dioxide fixation, dinitrogen fixation, pH tolerance, heavy metal detoxification, and oxidative stress defense were detected. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LJBT00000000.

Effect of carbon dioxide and bicarbonate as inorganic carbon sources on growth and adaptation of autohydrogenotrophic denitrifying bacteria

Energy Technology Data Exchange (ETDEWEB)

Ghafari, Shahin; Hasan, Masitah [Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur (Malaysia); Aroua, Mohamed Kheireddine [Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur (Malaysia)], E-mail: mk_aroua@um.edu.my

2009-03-15

Acclimation of autohydrogenotrophic denitrifying bacteria using inorganic carbon source (CO{sub 2} and bicarbonate) and hydrogen gas as electron donor was performed in this study. In this regard, activated sludge was used as the seed source and sequencing batch reactor (SBR) technique was applied for accomplishing the acclimatization. Three distinct strategies in feeding of carbon sources were applied: (I) continuous sparging of CO{sub 2}, (II) bicarbonate plus continuous sparging of CO{sub 2}, and (III) only bicarbonate. The pH-reducing nature of CO{sub 2} showed an unfavorable impact on denitrification rate; however bicarbonate resulted in a buffered environment in the mixed liquor and provided a suitable mean to maintain the pH in the desirable range of 7-8.2. As a result, bicarbonate as the only carbon source showed a faster adaptation, while carbon dioxide as the only carbon source as well as a complementary carbon source added to bicarbonate resulted in longer acclimation period. Adapted hydrogenotrophic denitrifying bacteria, using bicarbonate and hydrogen gas in the aforementioned pH range, caused denitrification at a rate of 13.33 mg NO{sub 3}{sup -}-N/g MLVSS/h for degrading 20 and 30 mg NO{sub 3}{sup -}-N/L and 9.09 mg NO{sub 3}{sup -}-N/g MLVSS/h for degrading 50 mg NO{sub 3}{sup -}-N/L.

Chromium isotopes in carbonates — A tracer for climate change and for reconstructing the redox state of ancient seawater

DEFF Research Database (Denmark)

Frei, Robert; Gaucher, Claudio; Døssing, Lasse Nørbye

2011-01-01

Strontium and carbon isotopes of marine carbonates are routinely applied for chemostratigraphic cross correlations of time-equivalent sedimentary sequences and for calibration of the compositional evolution of seawater throughout Earth's history, mainly for the purpose of reconstructing ancient c...

Cambrian-lower Middle Ordovician passive carbonate margin, southern Appalachians: Chapter 14

Science.gov (United States)

Read, J. Fred; Repetski, John E.

2012-01-01

The southern Appalachian part of the Cambrian–Ordovician passive margin succession of the great American carbonate bank extends from the Lower Cambrian to the lower Middle Ordovician, is as much as 3.5 km (2.2 mi) thick, and has long-term subsidence rates exceeding 5 cm (2 in.)/k.y. Subsiding depocenters separated by arches controlled sediment thickness. The succession consists of five supersequences, each of which contains several third-order sequences, and numerous meter-scale parasequences. Siliciclastic-prone supersequence 1 (Lower Cambrian Chilhowee Group fluvial rift clastics grading up into shelf siliciclastics) underlies the passive margin carbonates. Supersequence 2 consists of the Lower Cambrian Shady Dolomite–Rome-Waynesboro Formations. This is a shallowing-upward ramp succession of thinly bedded to nodular lime mudstones up into carbonate mud-mound facies, overlain by lowstand quartzose carbonates, and then a rimmed shelf succession capped by highly cyclic regressive carbonates and red beds (Rome-Waynesboro Formations). Foreslope facies include megabreccias, grainstone, and thin-bedded carbonate turbidites and deep-water rhythmites. Supersequence 3 rests on a major unconformity and consists of a Middle Cambrian differentiated rimmed shelf carbonate with highly cyclic facies (Elbrook Formation) extending in from the rim and passing via an oolitic ramp into a large structurally controlled intrashelf basin (Conasauga Shale). Filling of the intrashelf basin caused widespread deposition of thin quartz sandstones at the base of supersequence 4, overlain by widespread cyclic carbonates (Upper Cambrian lower Knox Group Copper Ridge Dolomite in the south; Conococheague Formation in the north). Supersequence 5 (Lower Ordovician upper Knox in the south; Lower to Middle Ordovician Beekmantown Group in the north) has a basal quartz sandstone-prone unit, overlain by cyclic ramp carbonates, that grade downdip into thrombolite grainstone and then storm

Interaction of carbon nano tubes with DNA segments

International Nuclear Information System (INIS)

Peressinotto, Valdirene Sullas Teixeira

2007-01-01

Single- and double-stranded DNA (deoxyribonucleic acid) molecules can strongly bind to single-walled carbon nanotubes (SWNT) via non-covalent interactions. Under certain conditions, the DNA molecule spontaneously self-assembles into a helical wrapping around the tubular structure of the carbon nanotubes to form DNA/SWNT hybrids, which are both stable and soluble in water. This system has recently received extensive attention, since, besides rendering SWNTs dispersible in water as individual tubes, the DNA hybrids are very promising candidates for many applications in nanotechnology and molecular biology. All the possible applications for DNA-SWNT hybrids require, however, a fully understanding of DNA-nanotube wrapping mechanism which is still lacking in the literature. In this context, the aim of this work was to investigate the non-covalent interaction in aqueous medium between SWNTs and synthetic DNA segments having a known nucleotide sequence. Initially, the study was focused on poly d(GT)n sequences (n = 10, 30 and 45) that contain a sequence of alternating guanine and thymine bases and for which the efficiency to disperse and separate carbon nanotubes has already been demonstrated. Besides the size of GT sequences, the effects of ionic strength and pH in the interaction were also investigated. Afterwards, we studied the interaction of SWNT with DNA molecules that contain only a single type of nitrogenous base (DNA homopolymers), which has not been reported in details in the literature. We investigated homopolymers of poly dA 20 , poly dT 20 , poly dC 20 and the duplex poly dA 20 :dT 20 . Most of the study was carried out with small-diameter HiPco SWNTs (with diameters between 0.7 and 1.2 nm). In some studies, SWNTs with diameter around 1.4 nm, synthesized via laser ablation and arc-discharge methods, were also investigated. The arc-discharge nanotubes used in this study were functionalized with carboxylic groups (-COOH) due to their purification using strong

Sedimentary facies analysis of a high-frequency, small-scale, peritidal carbonate sequence in the Lower Jurassic of the Tripolis carbonate unit (central western Crete, Greece: Long-lasting emergence and fossil laminar dolocretes horizons

Directory of Open Access Journals (Sweden)

Fotini A. Pomoni

2016-07-01

Full Text Available The study examines a Lower Jurassic (late Liassic cyclic lagoonal–peritidal stratigraphic unit outcropping in central western Crete (Tripolis unit, which corresponds to the eastern (internal part of the mainland Gavrovo-Tripolis platform, the most significant external platform of the Hellenides. The studied Tripolis carbonate sequence consists of meter-scale, shallowing-upward successions of restricted inner-carbonate platform facies, including cyclically repeated subtidal, intertidal and supratidal facies, that are separated by erosion surfaces (elementary cycles. Each cycle starts with relatively open-marine facies, which are overlain by shallower, more restricted facies (tidal flat progradation. The lithofacies association includes dolomitic intraclastic–peloidal–bioclastic wackestones–packstones/floatstones and grainstones/rudstones dominated by a restricted shallow-marine fauna (bivalves, gastropods, ostracods and seldom benthic foraminifers, representing a shallow subtidal to intertidal, moderately high-energy environment within an inner-platform setting (peritidal environment to restricted lagoon. This lithofacies association has been intermittently subaerially exposed and has undergone diagenetic processes in an inter- or supratidal environment, exhibiting features of vadose diagenesis and pedogenesis due to long-lasting exposure along certain horizons. The peritidal facies are capped by dolocretes controlled by root-activities (laminar dolocretes, peloidal–pisoid dolocretes and massive dolocretes, marking the end of each depositional cycle, and, thus, distinguishing the successive episodes of a prolonged subaerial exposure period and birth of paleosol horizons. Dolocretes consist a diagenetic facies, characterized by several vadose and pedogenic fabrics, including fenestral cavities with geopetal structures, “flower spar” to blocky sparry cement in primary pores, micritic coatings, crudely pelleted walls, alveolar

Carbon fibre and nitinol needles for MRI-guided interventions: First in vitro and in vivo application

Energy Technology Data Exchange (ETDEWEB)

Thomas, Christoph, E-mail: Christoph.thomas@med.uni-tuebingen.de [Department of Diagnostic and Interventional Radiology, University of Tuebingen, Hoppe-Seyler-Strasse 3, 72076 Tuebingen (Germany); Wojtczyk, Hanne [Section of Experimental Radiology, University of Tuebingen, Hoppe-Seyler-Strasse 3, 72076 Tuebingen (Germany); Rempp, Hansjoerg; Clasen, Stephan; Horger, Marius [Department of Diagnostic and Interventional Radiology, University of Tuebingen, Hoppe-Seyler-Strasse 3, 72076 Tuebingen (Germany); Lassberg, Christoph von [Department of Sports Medicine, University of Tuebingen, Silcherstrasse 5, 72076 Tuebingen (Germany); Fritz, Jan [Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287 (United States); Claussen, Claus D. [Department of Diagnostic and Interventional Radiology, University of Tuebingen, Hoppe-Seyler-Strasse 3, 72076 Tuebingen (Germany); Pereira, Philippe L. [Department of Radiology, Minimally Invasive Therapies and Nuclearmedicine, SLK-Kliniken Heilbronn GmbH, Am Gesundbrunnen 20-26, 74078 Heilbronn (Germany)

2011-09-15

Objective: To assess the artefact properties of a MR-compatible carbon fibre needle with a nitinol mandrin in vitro and to report first clinical experiences. Materials and methods: In vitro, the carbon fibre/nitinol needle was imaged at different angles against the main magnetic field (1.5 T open bore magnet). A gradient echo MR fluoroscopy sequence (GRE: TR 9.3 ms, TE 3.12 ms, bandwidth 200 Hz/pixel, flip-angle 12{sup o}) and a fast turbo spin echo sequence (FSE: TR 412 ms, TE 9.7 ms, bandwidth 200 Hz/pixel, flip-angle 150{sup o}) were used. Artefact width, needle intensity contrast and needle tip location errors were assessed. In vivo, lumbar periradicular corticosteroid injections and one sclerotherapy were performed with carbon fibre needles (10 procedures) and with titanium alloy needles (2 procedures). The artefact sizes and contrasts were measured. Results: In vitro, artefact diameters of the carbon fibre needle ranged from 3.3 to 4.6 mm, contrasts from 0.11 to 0.52, with larger artefact contrasts and widths with the GRE sequence. Needle tip location errors of -2.1 to -2.8 mm were observed. Decreasing angles to the main field lead to smaller artefacts. In vivo, the carbon fibre/nitinol needle produced smaller artefacts (mean width FSE/GRE: 2.8 mm/4.6 mm) with lower contrast (0.30-0.42) than the titanium alloy needle (mean width FSE/GRE: 4.1 mm/7.5 mm, contrast 0.60-0.73). Conclusions: The carbon fibre/nitinol needle is useful for performing MR-guided interventions at 1.5 T, producing more subtle artefacts than a titanium alloy needle, but with an incomplete depiction and thus inaccurate localization of the needle tip.

Massive stars on the verge of exploding: the properties of oxygen sequence Wolf-Rayet stars

NARCIS (Netherlands)

Tramper, F.; Straal, S.M.; Sanyal, D.; Sana, H.; de Koter, A.; Gräfener, G.; Langer, N.; Vink, J.S.; de Mink, S.E.; Kaper, L.

2015-01-01

Context. Oxygen sequence Wolf-Rayet (WO) stars are a very rare stage in the evolution of massive stars. Their spectra show strong emission lines of helium-burning products, in particular highly ionized carbon and oxygen. The properties of WO stars can be used to provide unique constraints on the

Universal sequence map (USM of arbitrary discrete sequences

Directory of Open Access Journals (Sweden)

Almeida Jonas S

2002-02-01

Full Text Available Abstract Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. Results We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM, is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR. The latter enables the representation of 4 unit type sequences (like DNA as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. Conclusions USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules.

Sedimentology and sequence stratigraphy of the Lopingian (Late Permian) coal measures in southwestern China

Energy Technology Data Exchange (ETDEWEB)

Wang, Hao [School of Geosciences and Surveying Engineering, China University of Mining and Technology, Beijing (China); School of Earth and Environment, University of Leeds (United Kingdom); Shao, Longyi; Hao, Liming; Zhang, Pengfei [School of Geosciences and Surveying Engineering, China University of Mining and Technology, Beijing (China); Glasspool, Ian J. [Department of Geology, Field Museum of Natural History, Chicago, Illinois (United States); Wheeley, James R.; Hilton, Jason [School of Geography, Earth and Environmental Sciences, University of Birmingham (United Kingdom); Wignall, Paul B. [School of Earth and Environment, University of Leeds (United Kingdom); Yi, Tongsheng [Guizhou Bureau of Coal Geological Exploration, Guiyang, Guizhou (China); Zhang, Mingquan [Coal Geology and Prospecting Institute of Yunnan Province, Kunming, Yunnan (China)

2011-01-01

The Lopingian coal measures of southwestern China were deposited within a range of facies associations spanning a spectrum of settings from fluvial to marine carbonate platform. The transitional to terrestrial coal measures are dominated by siliciclastics, but they also contain fifteen laterally extensive marine bands (limestone beds and mudstone). These bands act as marker horizons that enable correlation between fully marine and terrestrial facies. Examination of this range of facies and their sedimentology has enabled the development of a high-resolution sequence stratigraphic framework. Set against the established backdrop of second-order Lopingian transgression, sixteen fourth-order sequences and three composite sequences (third-order) are recognized. Results show that, in the composite sequences, peat accumulation in the seaward parts of the study area predominantly correlates with early transgressive sequence sets (TSS), while in more landward areas it correlates with the middle TSS to late highstand sequence sets (HSS). Differences in peat-accumulation regimes within the sequence stratigraphic framework are attributed to variations in subsidence and background siliciclastic input rates in different depositional settings, with these combining to produce differences in the rate of accommodation change. The preservation of coal resources in the middle to late HSS in this area was most likely related to the rise of the regional base level throughout the Lopingian. (author)

Is sequence awareness mandatory for perceptual sequence learning: An assessment using a pure perceptual sequence learning design.

Science.gov (United States)

Deroost, Natacha; Coomans, Daphné

2018-02-01

We examined the role of sequence awareness in a pure perceptual sequence learning design. Participants had to react to the target's colour that changed according to a perceptual sequence. By varying the mapping of the target's colour onto the response keys, motor responses changed randomly. The effect of sequence awareness on perceptual sequence learning was determined by manipulating the learning instructions (explicit versus implicit) and assessing the amount of sequence awareness after the experiment. In the explicit instruction condition (n = 15), participants were instructed to intentionally search for the colour sequence, whereas in the implicit instruction condition (n = 15), they were left uninformed about the sequenced nature of the task. Sequence awareness after the sequence learning task was tested by means of a questionnaire and the process-dissociation-procedure. The results showed that the instruction manipulation had no effect on the amount of perceptual sequence learning. Based on their report to have actively applied their sequence knowledge during the experiment, participants were subsequently regrouped in a sequence strategy group (n = 14, of which 4 participants from the implicit instruction condition and 10 participants from the explicit instruction condition) and a no-sequence strategy group (n = 16, of which 11 participants from the implicit instruction condition and 5 participants from the explicit instruction condition). Only participants of the sequence strategy group showed reliable perceptual sequence learning and sequence awareness. These results indicate that perceptual sequence learning depends upon the continuous employment of strategic cognitive control processes on sequence knowledge. Sequence awareness is suggested to be a necessary but not sufficient condition for perceptual learning to take place. Copyright © 2018 Elsevier B.V. All rights reserved.

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

Science.gov (United States)

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

2016-03-01

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

Low-mass stars with mass loss and low-luminosity carbon star formation

International Nuclear Information System (INIS)

Boothroyd, A.I.

1987-01-01

The effects of large carbon enrichments in static stellar envelopes were investigated, using new Los Alamos opacities (including low-temperature carbon and molecular opacities) and including carbon ionizations. To search for the production of low-mass,low-luminosity carbon stars, detailed stellar evolutionary computations were carried out for a grid of low-mass stars of two different metallicities. The stars were evolved from the main sequence through all intermediate stages and through helium-shell flashes on the asymptotic giant branch. The effects of the latest nuclear reaction rates, the new Los Alamos opacities, Reimers-type wind mass loss, and detailed treatment of convection and semi-convection were investigated. Two low-luminosity carbon stars were achieved, in excellent agreement with observations. Conditions favoring dredge-up (and thus carbon-star production) include a reasonably large convective mixing length, low metallicity, relatively large envelope mass, and high flash strength. Mass loss was of major importance, tending to oppose dredge-up; the total mass-loss amounts inferred from observations suffice to prevent formation of high-mass, high-luminosity carbon stars

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir.

Science.gov (United States)

Freedman, Adam J E; Tan, BoonFei; Thompson, Janelle R

2017-06-01

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 , harbor a 'deep carbonated biosphere' with carbon cycling potential. We sampled subsurface fluids from scCO 2 -water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Bromine isotopic signature facilitates de novo sequencing of peptides in free-radical-initiated peptide sequencing (FRIPS) mass spectrometry.

Science.gov (United States)

Nam, Jungjoo; Kwon, Hyuksu; Jang, Inae; Jeon, Aeran; Moon, Jingyu; Lee, Sun Young; Kang, Dukjin; Han, Sang Yun; Moon, Bongjin; Oh, Han Bin

2015-02-01

We recently showed that free-radical-initiated peptide sequencing mass spectrometry (FRIPS MS) assisted by the remarkable thermochemical stability of (2,2,6,6-tetramethyl-piperidin-1-yl)oxyl (TEMPO) is another attractive radical-driven peptide fragmentation MS tool. Facile homolytic cleavage of the bond between the benzylic carbon and the oxygen of the TEMPO moiety in o-TEMPO-Bz-C(O)-peptide and the high reactivity of the benzylic radical species generated in •Bz-C(O)-peptide are key elements leading to extensive radical-driven peptide backbone fragmentation. In the present study, we demonstrate that the incorporation of bromine into the benzene ring, i.e. o-TEMPO-Bz(Br)-C(O)-peptide, allows unambiguous distinction of the N-terminal peptide fragments from the C-terminal fragments through the unique bromine doublet isotopic signature. Furthermore, bromine substitution does not alter the overall radical-driven peptide backbone dissociation pathways of o-TEMPO-Bz-C(O)-peptide. From a practical perspective, the presence of the bromine isotopic signature in the N-terminal peptide fragments in TEMPO-assisted FRIPS MS represents a useful and cost-effective opportunity for de novo peptide sequencing. Copyright © 2015 John Wiley & Sons, Ltd.

Complete genome sequence of Mahella australiensis type strain (50-1 BONT)

Energy Technology Data Exchange (ETDEWEB)

Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Ngatchou, Olivier Duplex [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Pukall, Rudiger [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Abt, Birte [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute

2011-01-01

Mahella australiensis Bonilla Salinas et al. 2004 is the type species of the genus Mahella, which belongs to the family Thermoanaerobacteraceae. The species is of interest because it differs from other known anaerobic spore-forming bacteria in its G+C content, and in certain phenotypic traits, such as carbon source utilization and relationship to temperature. Moreo- ver, it has been discussed that this species might be an indigenous member of petroleum and oil reservoirs. This is the first completed genome sequence of a member of the genus Mahella and the ninth completed type strain genome sequence from the family Thermoanaerobacte- raceae. The 3,135,972 bp long genome with its 2,974 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Design and control of an alternative distillation sequence for bioethanol purification

DEFF Research Database (Denmark)

Errico, Massimiliano; Ramírez-Márquez, César; Torres Ortega, Carlo Edgar

2015-01-01

BACKGROUND: Bioethanol is a green fuel considered to be a sustainable alternative to petro-derived gasoline. The transport sector contributes significantly to carbon dioxide emission and consequently has a negative impact on the air quality and is responsible for the increase of the greenhouse...... separation is presented. The steady state performance and the dynamic beavior are analyzed compared with the classical configuration reported in the literature. RESULTS: Ethanol-water azeotropic separation represents a challenge for bioethanol purification. Usually a three column sequence is used to obtain...... fuel grade bioethanol by extractive distillation. In order to reduce bioethanol purification cost a two column separation sequence is proposed. This configuration shows a 10% saving in capital costs together with higher ethanol recovery and better control properties compared with the classical three...

Synthesis of tetrahydrokhusitone. Annulation of the cyclohexane ring by free radical and carbanionic sequence of reactions

Directory of Open Access Journals (Sweden)

ZIVORAD CEKOVIC

2003-05-01

Full Text Available The synthesis of norcadinane sesquiterpene tetrahydrokhusitone 1 has been achieved by a new method for annulation of cyclohexane ring involving a sequence of free radical d-alkylation of the non-activated carbon atom and intramolecular carbanionic alkylation. (–-Menthol was used as the starting compound.

Molecular Cloning and Characterization of Carbonic Anhydrase XII from Pufferfish (Takifugu rubripes

Directory of Open Access Journals (Sweden)

Kanij Rukshana Sumi

2018-03-01

Full Text Available In this study, an 1888-bp carbonic anhydrase XII (CA XII sequence was cloned from the brain of the pufferfish, Takifugu rubripes. The cloned sequence contained a coding region of 1470-bp, which was predicted to translate into a protein of 490 amino acid residues. The predicted protein showed between 68–56% identity with the large yellow croaker (Larimichthys crocea, tilapia (Oreochromis niloticus, and Asian arowana (Scleropages formosus CA XII proteins. It also exhibited 36% and 53% identity with human CA II and CA XII, respectively. The cloned sequence contained a 22 amino acid NH2-terminal signal sequence and three Asn-Xaa-Ser/Thr sequons, among which one was potentially glycosylated. Four cysteine residues were also identified (Cys-21, Cys-201, Cys-355, and Cys-358, two of which (Cys-21 and Cys-201 could potentially form a disulfide bond. A 22-amino acid COOH-terminal cytoplasmic tail containing a potential site for phosphorylation by protein kinase A was also found. The cloned sequence might be a transmembrane protein, as predicted from in silico and phylogenetic analyses. The active site analysis of the predicted protein showed that its active site residues were highly conserved with tilapia CA XII protein. Homology modeling of the pufferfish CA XII was done using the crystal structure of the extracellular domain of human carbonic anhydrase XII at 1.55 Å resolution as a template. Semi-quantitative reverse transcription (RT-PCR, quantitative PCR (q-PCR, and in situ hybridization confirmed that pufferfish CA XII is highly expressed in the brain.

On the mechanism of water cluster-ion formation in carbon dioxide

International Nuclear Information System (INIS)

Warneck, P.; Rakshit, A.B.

1981-01-01

A drift chamber mass spectrometer has been used to study the formation of water cluster-ions in carbon dioxide containing traces of water vapour. The dominant reaction sequences were identified up to the fourth generation of daughter ions starting with CO 2 + . The subsequent reaction mechanism remains uncertain and several possibilities are discussed. The final ions are H 3 O + H 2 O and H 3 O + (H 2 O) 2 . The significance of the reaction schemes to the radiation chemistry of carbon dioxide is pointed out. (orig.)

Carbon Partitioning in Green Algae (Chlorophyta and the Enolase Enzyme

Directory of Open Access Journals (Sweden)

Jürgen E. W. Polle

2014-08-01

Full Text Available The exact mechanisms underlying the distribution of fixed carbon within photoautotrophic cells, also referred to as carbon partitioning, and the subcellular localization of many enzymes involved in carbon metabolism are still unknown. In contrast to the majority of investigated green algae, higher plants have multiple isoforms of the glycolytic enolase enzyme, which are differentially regulated in higher plants. Here we report on the number of gene copies coding for the enolase in several genomes of species spanning the major classes of green algae. Our genomic analysis of several green algae revealed the presence of only one gene coding for a glycolytic enolase [EC 4.2.1.11]. Our predicted cytosolic localization would require export of organic carbon from the plastid to provide substrate for the enolase and subsequent re-import of organic carbon back into the plastids. Further, our comparative sequence study of the enolase and its 3D-structure prediction may suggest that the N-terminal extension found in green algal enolases could be involved in regulation of the enolase activity. In summary, we propose that the enolase represents one of the crucial regulatory bottlenecks in carbon partitioning in green algae.

Responses of Carbon Dynamics to Nitrogen Deposition in Typical Freshwater Wetland of Sanjiang Plain

Directory of Open Access Journals (Sweden)

Yang Wang

2014-01-01

Full Text Available The effects of nitrogen deposition (N-deposition on the carbon dynamics in typical Calamagrostis angustifolia wetland of Sanjiang Plain were studied by a pot-culture experiment during two continuous plant growing seasons. Elevated atmospheric N-deposition caused significant increases in the aboveground net primary production and root biomass; moreover, a preferential partition of carbon to root was also observed. Different soil carbon fractions gained due to elevated N-deposition and their response intensities followed the sequence of labile carbon > dissolved organic carbon > microbial biomass carbon, and the interaction between N-deposition and flooded condition facilitated the release of different carbon fractions. Positive correlations were found between CO2 and CH4 fluxes and liable carbon contents with N-deposition, and flooded condition also tended to facilitate CH4 fluxes and to inhibit the CO2 fluxes with N-deposition. The increases in soil carbon fractions occurring in the nitrogen treatments were significantly correlated with increases in root, aboveground parts, total biomass, and their carbon uptake. Our results suggested that N-deposition could enhance the contents of active carbon fractions in soil system and carbon accumulation in plant of the freshwater wetlands.

Cenozoic global sea level, sequences, and the New Jersey transect: Results from coastal plain and continental slope drilling

Science.gov (United States)

Miller, K.G.; Mountain, Gregory S.; Browning, J.V.; Kominz, M.; Sugarman, P.J.; Christie-Blick, N.; Katz, M.E.; Wright, J.D.

1998-01-01

high pelagic input associated with warm climates resulted in widespread carbonate deposition and thin sequences. Late middle Eocene and earliest Oligocene cooling events curtailed carbonate deposition in the coastal plain and slope, respectively, resulting in a switch to siliciclastic sedimentation. In onshore areas, Oligocene sequences are thin owing to low siliciclastic and pelagic input, and their distribution is patchy, reflecting migration or progradation of depocenters; in contrast, Miocene onshore sequences are thicker, reflecting increased sediment supply, and they are more complete downdip owing to simple tectonics. We conclude that the New Jersey margin provides a natural laboratory for unraveling complex interactions of eustasy, tectonics, changes in sediment supply, and climate change.

Geologic map showing springs rich in carbon dioxide or or chloride in California

Science.gov (United States)

Barnes, Ivan; Irwin, William P.; Gibson, H.A.

1975-01-01

Carbon dioxide- and chloride-rich springs occur in all geologic provinces in California, but are most abundant in the Coast Ranges and the Great Valley. The carbon-dioxide-rich springs issue mainly from Franciscan terrane; they also are rich in boron and are of the metamorphic type (White, 1957). Based on isotopic data, either the carbon dioxide or the water, or both, may be of metamorphic origin. Because of high magnesium values, the water of many of the carbon-dioxide-rich springs is thought to have passed through serpentinite. The chloride-rich waters are most common in rocks of the Great Valley sequence. Nearly all are more dilute than present-day sea water. The similarity in isotopic compositions of the metamorphic carbon-dioxide-rich water and the chloride-rich water may indicate a similar extent of water-rock interaction.

Complete genome sequence of Desulfomicrobium baculatum type strain (XT)

Energy Technology Data Exchange (ETDEWEB)

Copeland, Alex; Spring, Stefan; Goker, Markus; Schneider, Susanne; Lapidus, Alla; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C; Meincke, Linda; Sims, David; Brettin, Thomas; Detter, John C; Han, Cliff; Chain, Patrick; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C; Lucas, Susan

2009-05-20

Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain XT is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6percent (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Biostratigraphy and sequence stratigraphy of the Sarvak Formation at Fahliyan Anticline (South of Yasuj)

International Nuclear Information System (INIS)

Ahmadi, A.; Vaziri-Moghaddam, A.; Sayrafian, A.; Taheri, A.

2016-01-01

In this study, bio stratigraphy, depositional environment and sequence stratigraphy of the Sarvak Formation at Fahliyan Anticline was studied. 8 species of benthic foraminifera (4 genera) and 8 species of planktonic foraminifera (11 genera) in the study area were recognized. 6 biozones have been recognized by distribution of the foraminifera, which in stratigraphic order are: Favusella washitensis Zone, Orbitolina-Alveolinids Assemblage Zone, Rudist debris Zone, Oligostegina flood Zone, Whiteinella archaeocretacea Zone and Helvetoglobotruncana helvetica Zone. On the basis of these, the age of Albian–Turonian was considered for the Sarvak Formation. Based on petrography and analysis of microfacies features 9 different microfacies types have been recognized, which can be grouped into 3 depositional environments: lagoon, shoal and open marine. The Sarvak Formation represents sedimentation on a carbonate ramp. Sequence stratigraphy analysis led to identification of 4 third-order sequences.

NEW COOLING SEQUENCES FOR OLD WHITE DWARFS

International Nuclear Information System (INIS)

Renedo, I.; Althaus, L. G.; GarcIa-Berro, E.; Miller Bertolami, M. M.; Romero, A. D.; Corsico, A. H.; Rohrmann, R. D.

2010-01-01

We present full evolutionary calculations appropriate for the study of hydrogen-rich DA white dwarfs. This is done by evolving white dwarf progenitors from the zero-age main sequence, through the core hydrogen-burning phase, the helium-burning phase, and the thermally pulsing asymptotic giant branch phase to the white dwarf stage. Complete evolutionary sequences are computed for a wide range of stellar masses and for two different metallicities, Z = 0.01, which is representative of the solar neighborhood, and Z = 0.001, which is appropriate for the study of old stellar systems, like globular clusters. During the white dwarf cooling stage, we self-consistently compute the phase in which nuclear reactions are still important, the diffusive evolution of the elements in the outer layers and, finally, we also take into account all the relevant energy sources in the deep interior of the white dwarf, such as the release of latent heat and the release of gravitational energy due to carbon-oxygen phase separation upon crystallization. We also provide colors and magnitudes for these sequences, based on a new set of improved non-gray white dwarf model atmospheres, which include the most up-to-date physical inputs like the Lyα quasi-molecular opacity. The calculations are extended down to an effective temperature of 2500 K. Our calculations provide a homogeneous set of evolutionary cooling tracks appropriate for mass and age determinations of old DA white dwarfs and for white dwarf cosmochronology of the different Galactic populations.

Microbial Carbonic Anhydrases in Biomimetic Carbon Sequestration for Mitigating Global Warming: Prospects and Perspectives

Directory of Open Access Journals (Sweden)

Himadri Bose

2017-08-01

Full Text Available All the leading cities in the world are slowly becoming inhospitable for human life with global warming playing havoc with the living conditions. Biomineralization of carbon dioxide using carbonic anhydrase (CA is one of the most economical methods for mitigating global warming. The burning of fossil fuels results in the emission of large quantities of flue gas. The temperature of flue gas is quite high. Alkaline conditions are necessary for CaCO3 precipitation in the mineralization process. In order to use CAs for biomimetic carbon sequestration, thermo-alkali-stable CAs are, therefore, essential. CAs must be stable in the presence of various flue gas contaminants too. The extreme environments on earth harbor a variety of polyextremophilic microbes that are rich sources of thermo-alkali-stable CAs. CAs are the fastest among the known enzymes, which are of six basic types with no apparent sequence homology, thus represent an elegant example of convergent evolution. The current review focuses on the utility of thermo-alkali-stable CAs in biomineralization based strategies. A variety of roles that CAs play in various living organisms, the use of CA inhibitors as drug targets and strategies for overproduction of CAs to meet the demand are also briefly discussed.

Microbial Carbonic Anhydrases in Biomimetic Carbon Sequestration for Mitigating Global Warming: Prospects and Perspectives.

Science.gov (United States)

Bose, Himadri; Satyanarayana, Tulasi

2017-01-01

All the leading cities in the world are slowly becoming inhospitable for human life with global warming playing havoc with the living conditions. Biomineralization of carbon dioxide using carbonic anhydrase (CA) is one of the most economical methods for mitigating global warming. The burning of fossil fuels results in the emission of large quantities of flue gas. The temperature of flue gas is quite high. Alkaline conditions are necessary for CaCO 3 precipitation in the mineralization process. In order to use CAs for biomimetic carbon sequestration, thermo-alkali-stable CAs are, therefore, essential. CAs must be stable in the presence of various flue gas contaminants too. The extreme environments on earth harbor a variety of polyextremophilic microbes that are rich sources of thermo-alkali-stable CAs. CAs are the fastest among the known enzymes, which are of six basic types with no apparent sequence homology, thus represent an elegant example of convergent evolution. The current review focuses on the utility of thermo-alkali-stable CAs in biomineralization based strategies. A variety of roles that CAs play in various living organisms, the use of CA inhibitors as drug targets and strategies for overproduction of CAs to meet the demand are also briefly discussed.

Acid mine drainage neutralization in a pilot sequencing batch reactor using limestone from a paper and pulp industry

CSIR Research Space (South Africa)

Vadapalli, VRK

2015-10-01

Full Text Available This study investigated the implications of using two grades of limestone from a paper and pulp industry for neutralization of acid mine drainage (AMD) in a pilot sequencing batch reactor (SBR). In this regard, two grades of calcium carbonate were...

Quantum-Sequencing: Fast electronic single DNA molecule sequencing

Science.gov (United States)

Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

2014-03-01

A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

Weathering controls on mechanisms of carbon storage in grassland soils

Science.gov (United States)

Masiello, C.A.; Chadwick, O.A.; Southon, J.; Torn, M.S.; Harden, J.W.

2004-01-01

On a sequence of soils developed under similar vegetation, temperature, and precipitation conditions, but with variations in mineralogical properties, we use organic carbon and 14C inventories to examine mineral protection of soil organic carbon. In these soils, 14C data indicate that the creation of slow-cycling carbon can be modeled as occurring through reaction of organic ligands with Al3+ and Fe3+ cations in the upper horizons, followed by sorption to amorphous inorganic Al compounds at depth. Only one of these processes, the chelation Al3+ and Fe3+ by organic ligands, is linked to large carbon stocks. Organic ligands stabilized by this process traverse the soil column as dissolved organic carbon (both from surface horizons and root exudates). At our moist grassland site, this chelation and transport process is very strongly correlated with the storage and long-term stabilization of soil organic carbon. Our 14C results show that the mechanisms of organic carbon transport and storage at this site follow a classic model previously believed to only be significant in a single soil order (Spodosols), and closely related to the presence of forests. The presence of this process in the grassland Alfisol, Inceptisol, and Mollisol soils of this chronosequence suggests that this process is a more significant control on organic carbon storage than previously thought. Copyright 2004 by the American Geophysical Union.

Depositional architecture and sequence stratigraphy of the Upper Jurassic Hanifa Formation, central Saudi Arabia

Science.gov (United States)

El-Sorogy, Abdelbaset; Al-Kahtany, Khaled; Almadani, Sattam; Tawfik, Mohamed

2018-03-01

To document the depositional architecture and sequence stratigraphy of the Upper Jurassic Hanifa Formation in central Saudi Arabia, three composite sections were examined, measured and thin section analysed at Al-Abakkayn, Sadous and Maashabah mountains. Fourteen microfacies types were identified, from wackestones to boundstones and which permits the recognition of five lithofacies associations in a carbonate platform. Lithofacies associations range from low energy, sponges, foraminifers and bioclastic burrowed offshoal deposits to moderate lithoclstic, peloidal and bioclastic foreshoal deposits in the lower part of the Hanifa while the upper part is dominated by corals, ooidal and peloidal high energy shoal deposits to moderate to low energy peloidal, stromatoporoids and other bioclastics back shoal deposits. The studied Hanifa Formation exhibits an obvious cyclicity, distinguishing from vertical variations in lithofacies types. These microfacies types are arranged in two third order sequences, the first sequence is equivalent to the lower part of the Hanifa Formation (Hawtah member) while the second one is equivalent to the upper part (Ulayyah member). Within these two sequences, there are three to six fourth-order high frequency sequences respectively in the studied sections.

Multimodal sequence learning.

Science.gov (United States)

Kemény, Ferenc; Meier, Beat

2016-02-01

While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

Fractionation between inorganic and organic carbon during the Lomagundi (2.22 2.1 Ga) carbon isotope excursion

Science.gov (United States)

Bekker, A.; Holmden, C.; Beukes, N. J.; Kenig, F.; Eglinton, B.; Patterson, W. P.

2008-07-01

The Lomagundi (2.22-2.1 Ga) positive carbon isotope excursion in shallow-marine sedimentary carbonates has been associated with the rise in atmospheric oxygen, but subsequent studies have demonstrated that the carbon isotope excursion was preceded by the rise in atmospheric oxygen. The amount of oxygen released to the exosphere during the Lomagundi excursion is constrained by the average global fractionation between inorganic and organic carbon, which is poorly characterized. Because dissolved inorganic and organic carbon reservoirs were arguably larger in the Paleoproterozoic ocean, at a time of lower solar luminosity and lower ocean redox state, decoupling between these two variables might be expected. We determined carbon isotope values of carbonate and organic matter in carbonates and shales of the Silverton Formation, South Africa and in the correlative Sengoma Argillite Formation, near the border in Botswana. These units were deposited between 2.22 and 2.06 Ga along the margin of the Kaapvaal Craton in an open-marine deltaic setting and experienced lower greenschist facies metamorphism. The prodelta to offshore marine shales are overlain by a subtidal carbonate sequence. Carbonates exhibit elevated 13C values ranging from 8.3 to 11.2‰ vs. VPDB consistent with deposition during the Lomagundi positive excursion. The total organic carbon (TOC) contents range from 0.01 to 0.6% and δ13C values range from - 24.8 to - 13.9‰. Thus, the isotopic fractionation between organic and carbonate carbon was on average 30.3 ± 2.8‰ ( n = 32) in the shallow-marine environment. The underlying Sengoma shales have highly variable TOC contents (0.14 to 21.94%) and δ13C values (- 33.7 to - 20.8‰) with an average of - 27.0 ± 3.0‰ ( n = 50). Considering that the shales were also deposited during the Lomagundi excursion, and taking δ13C values of the overlying carbonates as representative of the δ13C value of dissolved inorganic carbon during shale deposition, a carbon

A Natural Light/Dark Cycle Regulation of Carbon-Nitrogen Metabolism and Gene Expression in Rice Shoots.

Science.gov (United States)

Li, Haixing; Liang, Zhijun; Ding, Guangda; Shi, Lei; Xu, Fangsen; Cai, Hongmei

2016-01-01

Light and temperature are two particularly important environmental cues for plant survival. Carbon and nitrogen are two essential macronutrients required for plant growth and development, and cellular carbon and nitrogen metabolism must be tightly coordinated. In order to understand how the natural light/dark cycle regulates carbon and nitrogen metabolism in rice plants, we analyzed the photosynthesis, key carbon-nitrogen metabolites, and enzyme activities, and differentially expressed genes and miRNAs involved in the carbon and nitrogen metabolic pathway in rice shoots at the following times: 2:00, 6:00, 10:00, 14:00, 18:00, and 22:00. Our results indicated that more CO2 was fixed into carbohydrates by a high net photosynthetic rate, respiratory rate, and stomatal conductance in the daytime. Although high levels of the nitrate reductase activity, free ammonium and carbohydrates were exhibited in the daytime, the protein synthesis was not significantly facilitated by the light and temperature. In mRNA sequencing, the carbon and nitrogen metabolism-related differentially expressed genes were obtained, which could be divided into eight groups: photosynthesis, TCA cycle, sugar transport, sugar metabolism, nitrogen transport, nitrogen reduction, amino acid metabolism, and nitrogen regulation. Additionally, a total of 78,306 alternative splicing events have been identified, which primarily belong to alternative 5' donor sites, alternative 3' acceptor sites, intron retention, and exon skipping. In sRNA sequencing, four carbon and nitrogen metabolism-related miRNAs (osa-miR1440b, osa-miR2876-5p, osa-miR1877 and osa-miR5799) were determined to be regulated by natural light/dark cycle. The expression level analysis showed that the four carbon and nitrogen metabolism-related miRNAs negatively regulated their target genes. These results may provide a good strategy to study how natural light/dark cycle regulates carbon and nitrogen metabolism to ensure plant growth and

A natural light/dark cycle regulation of carbon-nitrogen metabolism and gene expression in rice shoots

Directory of Open Access Journals (Sweden)

Haixing Li

2016-08-01

Full Text Available Light and temperature are two particularly important environmental cues for plant survival. Carbon and nitrogen are two essential macronutrients required for plant growth and development, and cellular carbon and nitrogen metabolism must be tightly coordinated. In order to understand how the natural light/dark cycle regulates carbon and nitrogen metabolism in rice plants, we analyzed the photosynthesis, key carbon-nitrogen metabolites and enzyme activities, and differentially expressed genes and miRNAs involved in the carbon and nitrogen metabolic pathway in rice shoots at the following times: 2:00, 6:00, 10:00, 14:00, 18:00 and 22:00. Our results indicated that more CO2 was fixed into carbohydrates by a high net photosynthetic rate, respiratory rate and stomatal conductance in the daytime. Although high levels of the nitrate reductase activity, free ammonium and carbohydrates were exhibited in the daytime, the protein synthesis was not significantly facilitated by the light and temperature. In mRNA sequencing, the carbon and nitrogen metabolism-related differentially expressed genes were obtained, which could be divided into eight groups: photosynthesis, TCA cycle, sugar transport, sugar metabolism, nitrogen transport, nitrogen reduction, amino acid metabolism and nitrogen regulation. Additionally, a total of 78,306 alternative splicing events have been identified, which primarily belong to alternative 5' donor sites, alternative 3' acceptor sites, intron retention and exon skipping. In sRNA sequencing, four carbon and nitrogen metabolism-related miRNAs (osa-miR1440b, osa-miR2876-5p, osa-miR1877 and osa-miR5799 were determined to be regulated by natural light/dark cycle. The expression level analysis showed that the four carbon and nitrogen metabolism-related miRNAs negatively regulated their target genes. These results may provide a good strategy to study how natural light/dark cycle regulates carbon and nitrogen metabolism to ensure plant

Optical and mechanical excitation thermography for impact response in basalt-carbon hybrid fiber-reinforced composite laminates

OpenAIRE

Zhang, Hai; Sfarra, Stefano; Sarasini, Fabrizio; Ibarra-Castanedo, Clemente; Perilli, Stefano; Fernandes, Henrique; Duan, Yuxia; Peeters, Jeroen; Avelidis, Nicholas P; Maldague, Xavier

2017-01-01

Abstract: In this paper, optical and mechanical excitation thermography were used to investigate basalt fiber reinforced polymer (BFRP), carbon fiber reinforced polymer (CFRP) and basalt-carbon fiber hybrid specimens subjected to impact loading. Interestingly, two different hybrid structures including sandwich-like and intercalated stacking sequence were used. Pulsed phase thermography (PPT), principal component thermography (PCT) and partial least squares thermography (PLST) were used to pro...

Correlation between high resolution sequence stratigraphy and mechanical stratigraphy for enhanced fracture characteristic prediction

Science.gov (United States)

Al Kharusi, Laiyyan M.

Sequence stratigraphy relates changes in vertical and lateral facies distribution to relative changes in sea level. These relative changes in carbonates effect early diagenesis, types of pores, cementation and dissolution patterns. As a result, in carbonates, relative changes in sea level significantly impact the lithology, porosity, diagenesis, bed and bounding surfaces which are all factors that control fracture patterns. This study explores these relationships by integrating stratigraphy with fracture analysis and petrophysical properties. A special focus is given to the relationship between mechanical boundaries and sequence stratigraphic boundaries in three different settings: (1) Mississippian strata in Sheep Mountain Anticline, Wyoming, (2) Mississippian limestones in St. Louis, Missouri, and (3) Pennsylvanian limestones intermixed with elastics in the Paradox Basin, Utah. The analysis of these sections demonstrate that a fracture hierarchy exists in relation to the sequence stratigraphic hierarchy. The majority of fractures (80%) terminate at genetic unit boundaries or the internal flooding surface that separates the transgressive from regressive hemicycle. Fractures (20%) that do not terminate at genetic unit boundaries or their internal flooding surface terminate at lower order sequence stratigraphic boundaries or their internal flooding surfaces. Secondly, the fracture spacing relates well to bed thickness in mechanical units no greater than 0.5m in thickness but with increasing bed thickness a scatter from the linear trend is observed. In the Paradox Basin the influence of strain on fracture density is illustrated by two sections measured in different strain regimes. The folded strata at Raplee Anticline has higher fracture densities than the flat-lying beds at the Honaker Trail. Cemented low porosity rocks in the Paradox Basin do not show a correlation between fracture pattern and porosity. However velocity and rock stiffness moduli's display a slight

MRI contrast enhancement using Magnetic Carbon Nanoparticles

Science.gov (United States)

Chaudhary, Rakesh P.; Kangasniemi, Kim; Takahashi, Masaya; Mohanty, Samarendra K.; Koymen, Ali R.; Department of Physics, University of Texas at Arlington Team; University of Texas Southwestern Medical Center Team

2014-03-01

In recent years, nanotechnology has become one of the most exciting forefront fields in cancer diagnosis and therapeutics such as drug delivery, thermal therapy and detection of cancer. Here, we report development of core (Fe)-shell (carbon) nanoparticles with enhanced magnetic properties for contrast enhancement in MRI imaging. These new classes of magnetic carbon nanoparticles (MCNPs) are synthesized using a bottom-up approach in various organic solvents, using the electric plasma discharge generated in the cavitation field of an ultrasonic horn. Gradient echo MRI images of well-dispersed MCNP-solutions (in tube) were acquired. For T2 measurements, a multi echo spin echo sequence was performed. From the slope of the 1/T2 versus concentration plot, the R2 value for different CMCNP-samples was measured. Since MCNPs were found to be extremely non-reactive, and highly absorbing in NIR regime, development of carbon-based MRI contrast enhancement will allow its simultaneous use in biomedical applications. We aim to localize the MCNPs in targeted tissue regions by external DC magnetic field, followed by MRI imaging and subsequent photothermal therapy.

The ternary Fe-C-N system: Homogeneous distributions of nitrogen and carbon

DEFF Research Database (Denmark)

Brink, Bastian; Ståhl, Kenny; Christiansen, Thomas Lundin

2017-01-01

of the nitriding and carburizing potentials, tailored nitrogen and carbon contents can be achieved, which allows assessment of a phase stability diagram for the Fe-N-C system, for which available experimental data is limited. Thermal decomposition sequences were established for the various iron carbides and (carbo...

Comparative investigation on electrochemical behavior of hydroquinone at carbon ionic liquid electrode, ionic liquid modified carbon paste electrode and carbon paste electrode

International Nuclear Information System (INIS)

Zhang, Ya; Zheng, Jian Bin

2007-01-01

Ionic liquid, 1-heptyl-3-methylimidazolium hexafluorophosphate (HMIMPF 6 ), has been used to fabricate two new electrodes, carbon ionic liquid electrode (CILE) and ionic liquid modified carbon paste electrode (IL/CPE), using graphite powder mixed with HMIMPF 6 or the mixture of HMIMPF 6 /paraffin liquid as the binder, respectively. The electrochemical behaviors of hydroquinone at the CILE, the IL/CPE and the CPE were investigated in phosphate buffer solution. At all these electrodes, hydroquinone showed a pair of redox peaks. The order of the current response and the standard rate constant of hydroquinone at these electrodes were as follows: CILE > IL/CPE > CPE, while the peak-to-peak potential separation was in an opposite sequence: CILE < IL/CPE < CPE. The results show the superiority of CILE to IL/CPE and CPE, and IL/CPE to CPE in terms of promoting electron transfer, improving reversibility and enhancing sensitivity. The CILE was chosen as working electrode to determine hydroquinone by differential pulse voltammetry, which can be used for sensitive, simple and rapid determination of hydroquinone in medicated skin cosmetic cream

Tempo and scale of late Paleocene and early Eocene carbon isotope cycles: Implications for the origin of hyperthermals

Science.gov (United States)

Zachos, James C.; McCarren, Heather; Murphy, Brandon; Röhl, Ursula; Westerhold, Thomas

2010-10-01

The upper Paleocene and lower Eocene are marked by several prominent (> 1‰) carbon isotope (δ 13C) excursions (CIE) that coincide with transient global warmings, or thermal maxima, including the Paleocene-Eocene Thermal Maximum (PETM). The CIE, which are recorded mainly in marine sedimentary sequences, have also been identified in continental sequences, occurred episodically, and yet appear to be paced or triggered by orbital forcing. To constrain the timing and scale of the CIE relative to long-term baseline variability, we have constructed a 4.52 million year (myr) long, high-resolution (~ 3 kyr) bulk sediment carbon isotope record spanning the lower Eocene to upper Paleocene (C25r-C24n) from a pelagic sediment section recovered at ODP Site 1262 in the southeast Atlantic. This section, which was orbitally-tuned utilizing high-resolution core log physical property and geochemical records, is the most stratigraphically complete upper Paleocene to lower Eocene sequence recovered to date. Time-series analysis of the carbon isotope record along with a high-resolution Fe intensity record obtained by XRF core scanner reveal cyclicity with variance concentrated primarily in the precession (21 kyr) and eccentricity bands (100 and 400-kyr) throughout the upper Paleocene-lower Eocene. In general, minima in δ 13C correspond with peaks in Fe (i.e., carbonate dissolution), both of which appear to be in phase with maxima in eccentricity. This covariance is consistent with excess oceanic uptake of isotopically depleted carbon resulting in lower carbonate saturation during periods of high eccentricity. This relationship includes all late Paleocene and early Eocene CIE confirming pacing by orbital forcing. The lone exception is the PETM, which appears to be out of phase with the 400-kyr cycle, though possibly in phase with the 100-kyr cycle, reinforcing the notion that a mechanism other than orbital forcing and/or an additional source of carbon is required to account for the

Microbially-Mediated Precipitation of Calcium Carbonate Nanoparticles.

Science.gov (United States)

Kang, Ser Ku; Roh, Yul

2016-02-01

The objective of this study was to investigate the biomineralization of carbonate minerals using microorganisms (Wu Do-1) enriched from rhodoliths. A 16S rRNA sequence analysis showed that Wu Do-1 mainly contained Proteus mirabilis. The pH decreased from 6.5 to 5.3 over the first 4 days of incubation due to microbial oxidation of organic acids, after which it increased to 7.8 over the remaining incubation period. XRD analysis showed that the precipitates were Mg-rich cal- cite (MgxCa(1-x)CO3), whereas no precipitates were formed without the addition of Wu Do-1 in D-1 medium. SEM-EDS analyses showed that the Mg-rich calcite had a rhombohedron shape and consisted of Ca, Si and Mg with an extracelluar polymeric substance (EPS). In addition, TEM-EDS analyses revealed they were hexagon in shape, 500-700 nm in size, and composed of Ca, Mg, C, and O. These results indicated that Wu Do-1 induced precipitation of Mg-rich calcite on the cell walls and EPS via the accumulation of Ca and/or Mg ions. Therefore, microbial precipitation of carbonate nanoparticles may play an important role in metal and carbon biogeochemistry, as well as in carbon sequestration in natural environments.

Soil organic carbon assessments in cropping systems using isotopic techniques

Science.gov (United States)

Martín De Dios Herrero, Juan; Cruz Colazo, Juan; Guzman, María Laura; Saenz, Claudio; Sager, Ricardo; Sakadevan, Karuppan

2016-04-01

Introduction of improved farming practices are important to address the challenges of agricultural production, food security, climate change and resource use efficiency. The integration of livestock with crops provides many benefits including: (1) resource conservation, (2) ecosystem services, (3) soil quality improvements, and (4) risk reduction through diversification of enterprises. Integrated crop livestock systems (ICLS) with the combination of no-tillage and pastures are useful practices to enhance soil organic carbon (SOC) compared with continuous cropping systems (CCS). In this study, the SOC and its fractions in two cropping systems namely (1) ICLS, and (2) CCS were evaluated in Southern Santa Fe Province in Argentina, and the use of delta carbon-13 technique and soil physical fractionation were evaluated to identify sources of SOC in these systems. Two farms inside the same soil cartographic unit and landscape position in the region were compared. The ICLS farm produces lucerne (Medicago sativa Merrill) and oat (Avena sativa L.) grazed by cattle alternatively with grain summer crops sequence of soybean (Glicine max L.) and corn (Zea mays L.), and the farm under continuous cropping system (CCS) produces soybean and corn in a continuous sequence. The soil in the area is predominantly a Typic Hapludoll. Soil samples from 0-5 and 0-20 cm depths (n=4) after the harvest of grain crops were collected in each system and analyzed for total organic carbon (SOC, 0-2000 μm), particulate organic carbon (POC, 50-100 μm) and mineral organic carbon (MOC, is probably due to the presence of deep roots under pastures in ICLS. Delta carbon-13 values for 0-5 cm were -22.9, -21.2 and -19.9 per mil for REF, ICLS and CCS, respectively (Pis explained by the presence of tree species with high lignin content in natural vegetation. Lignin has lower delta carbon-13 compared to cellulose (dominating in crops and pastures), which is present in greater proportion in plant residues of

Carbonate petrography, kerogen distribution, and carbon and oxygen isotope variations in an early Proterozoic transition from limestone to iron-formation deposition, Transvaal Supergroup, South Africa

Science.gov (United States)

Beukes, N. J.; Klein, C.; Kaufman, A. J.; Hayes, J. M.

1990-01-01

The transition zone comprises Campbellrand microbialaminated (replacing "cryptalgalaminate") limestone and shale, with minor dolomite, conformably overlain by the Kuruman Iron Formation of which the basal part is characterized by siderite-rich microbanded iron-formation with minor magnetite and some hematite-containing units. The iron-formation contains subordinate intraclastic and microbialaminated siderite mesobands and was deposited in deeper water than the limestones. The sequence is virtually unaltered with diagenetic mineral assemblages reflecting a temperature interval of about 110 degrees to 170 degrees C and pressures of 2 kbars. Carbonate minerals in the different rock types are represented by primary micritic precipitates (now recrystallized to microsparite), early precompactional sparry cements and concretions, deep burial limpid euhedral sparites, and spar cements precipitated from metamorphic fluids in close contact with diabase sills. Paragenetic pathways of the carbonate minerals are broadly similar in all lithofacies with kerogen intimately associated with them. Kerogen occurs as pigmentation in carbonate crystals, as reworked organic detritus in clastic-textured carbonate units, and as segregations of kerogen pigment around late diagenetic carbonate crystals. Locally kerogen may also be replaced by carbonate spar. Carbon isotope compositions of the carbonate minerals and kerogen are dependent on their mode of occurrence and on the composition of the dominant carbonate species in a specific lithofacies. Integration of sedimentary, petrographic, geochemical, and isotopic results makes it possible to distinguish between depositional, early diagenetic, deep burial, and metamorphic effects on the isotopic compositions of the carbonate minerals and the kerogen in the sequence. Major conclusions are that deep burial thermal decarboxylation led to 13C depletion in euhedral ferroan sparites and 13C enrichment in kerogen (organic carbon). Metamorphic

Novel expressed sequence tag- simple sequence repeats (EST ...

African Journals Online (AJOL)

Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

RNA sequencing analysis reveals new findings of hyperbaric oxygen treatment on rats with acute carbon monoxide poisoning.

Science.gov (United States)

Wang, Wenlan; Xue, Li; Li, Ya; Li, Rong; Xie, Xiaoping; Bao, Junxiang; Hai, Chunxu; Li, Jinsheng

2016-01-01

To elucidate the altered gene network in the brains of carbon monoxide (CO) poisoned rats after treatment with hyperbaric oxygen (HBO₂). RNA sequencing (RNA-seq) analysis was performed to examine differentially expressed genes (DEGs) in brain tissue samples from nine male rats: a normal control group; a CO poisoning group; and an HBO₂ treatment group (three rats/group). Reverse transcription polymerase chain reaction (RT-PCR) and real-time quantitative PCR were used for validation of the DEGs in another 18 male rats (six rats/group). RNA-seq revealed that two genes were upregulated (4.18 and 8.76 log to the base 2 fold change) (p⟨0.05) in the CO-poisoned rats relative to the control rats; two genes were upregulated (3.88 and 7.69 log to the base 2 fold change); and 23 genes were downregulated (3.49-15.12 log to the base 2 fold change) (p⟨0.05) in the brains of the HBO₂-treated rats relative to the CO-poisoned rats. Target prediction of DEGs by gene network analysis and analysis of pathways affected suggested that regulation of gene expressions of dopamine metabolism and nitric oxide (NO) synthesis were significantly affected by CO poisoning and HBO₂ treatment. Results of RT-PCR and real-time quantitative PCR indicated that four genes (Pomc, GH-1, Pr1 and Fshβ) associated with hormone secretion in the hypothalamic-pituitary system have potential as markers for prognosis of CO. This study is the first RNA-seq analysis profile of HBO₂ treatment on rats with acute CO poisoning. It concludes that changes of hormone secretion in the hypothalamic-pituitary system, dopamine metabolism and NO synthesis involved in brain damage and behavior abnormalities after CO poisoning and HBO₂ therapy may regulate these changes.

Birth and demise of a Middle Jurassic isolated shallow-marine carbonate platform on a tilted fault block: Example from the Southern Iberian continental palaeomargin

Science.gov (United States)

Navarro, V.; Ruiz-Ortiz, P. A.; Molina, J. M.

2012-08-01

Subbetic Middle Jurassic oolitic limestones of the Jabalcuz Formation crop out in San Cristóbal hill, near Jaén city (Andalucía, Spain), between hemipelagic limestone and marl successions. The Jabalcuz limestones range in facies from calcareous breccias and micritic limestones to white cross-bedded oolitic limestones. Recent erosion has exhumed a Jurassic isolated shallow-water carbonate platform on the San Cristóbal hill. This shallow platform developed on a tilted fault block. An almost continuous, laterally extensive outcrop reveals tectono-sedimentary features distinctive of block-tilting in the different margins of the fault block. The studied sections represent various palaeogeographic positions in the ancient shallow-water carbonate platform and basin transition. This exceptional outcrop allows to decipher the triggering mechanisms of the birth, evolution, and drowning of this Jurassic isolated shallow-water carbonate platform. Two shallowing-upward depositional sequences separated by flooding surfaces can be distinguished on two different sides of the fault block. In the southeastern part of the outcrop, proximal sections grade vertically from distal talus fault breccias, with bivalve and serpulid buildup intercalations, to white cross-bedded oolitic limestones defining the lowermost depositional sequence. Upwards, overlying a flooding surface, the second sequence with oolitic limestones prograding over micritic deposits is recorded. In the southwest, oolitic, peloidal, and more distal micritic facies alternate, with notable southeastern progradation of oolitic facies in the upper part of the section, which represents the upper depositional sequence. The top of this second depositional sequence is another flooding surface recorded by the sedimentation of marls with radiolarians from the overlying formation. In the northwestern outcrops, the two depositional sequences are also almost completely preserved and can be differentiated. A 100 m

Carbon metabolic pathways in phototrophic bacteria and their broader evolutionary implications

Directory of Open Access Journals (Sweden)

Kuo-Hsiang eTang

2011-08-01

Full Text Available Photosynthesis is the biological process that converts solar energy to biomass, bio-products and biofuel. It is the only major natural solar energy storage mechanism on Earth. To satisfy the increased demand for sustainable energy sources and identify the mechanism of photosynthetic carbon assimilation, which is one of the bottlenecks in photosynthesis, it is essential to understand the process of solar energy storage and associated carbon metabolism in photosynthetic organisms. Researchers have employed physiological studies, microbiological chemistry, enzyme assays, genome sequencing, transcriptomics, and 13C-based metabolomics/fluxomics to investigate central carbon metabolism and enzymes that operate in phototrophs. In this report, we review diverse CO2 assimilation pathways, acetate assimilation, carbohydrate catabolism, the TCA cycle and some key and/or unconventional enzymes in central carbon metabolism of phototrophic microorganisms. We also discuss the reducing equivalent flow during photoautotrophic and photoheterotrophic growth, evolutionary links in the central carbon metabolic network, and correlations between photosynthetic and non-photosynthetic organisms. Considering the metabolic versatility in these fascinating and diverse photosynthetic bacteria, many essential questions in their central carbon metabolism still remain to be addressed.

Genome Sequence Databases (Overview): Sequencing and Assembly

Energy Technology Data Exchange (ETDEWEB)

Lapidus, Alla L.

2009-01-01

From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

Examination of the Thermo-mechanical Properties of E-Glass/Carbon Composites

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Hande Sezgin

2017-12-01

Full Text Available Eight-ply E-glass, carbon and E-glass/carbon fabric-reinforced polyester based hybrid composites were manufactured in this study. A vacuum infusion system was used as the production method. Dynamic mechanical analysis, thermogravimetric analysis and differential scanning calorimetry analysis were conducted to examine the thermo-mechanical properties of composite samples. The effect of reinforcement type and different stacking sequences of fabric plies on the thermo-mechanical properties of composite samples were also investigated. Results showed that the type and alignment of reinforcement material has a signifi cant effect on the dynamic mechanical properties of composite samples.

Sources and mobility of carbonate melts beneath cratons, with implications for deep carbon cycling, metasomatism and rift initiation

Science.gov (United States)

Tappe, Sebastian; Romer, Rolf L.; Stracke, Andreas; Steenfelt, Agnete; Smart, Katie A.; Muehlenbachs, Karlis; Torsvik, Trond H.

2017-05-01

Kimberlite and carbonatite magmas that intrude cratonic lithosphere are among the deepest probes of the terrestrial carbon cycle. Their co-existence on thick continental shields is commonly attributed to continuous partial melting sequences of carbonated peridotite at >150 km depths, possibly as deep as the mantle transition zone. At Tikiusaaq on the North Atlantic craton in West Greenland, approximately 160 Ma old ultrafresh kimberlite dykes and carbonatite sheets provide a rare opportunity to study the origin and evolution of carbonate-rich melts beneath cratons. Although their Sr-Nd-Hf-Pb-Li isotopic compositions suggest a common convecting upper mantle source that includes depleted and recycled oceanic crust components (e.g., negative ΔεHf coupled with > + 5 ‰ δ7Li), incompatible trace element modelling identifies only the kimberlites as near-primary low-degree partial melts (0.05-3%) of carbonated peridotite. In contrast, the trace element systematics of the carbonatites are difficult to reproduce by partial melting of carbonated peridotite, and the heavy carbon isotopic signatures (-3.6 to - 2.4 ‰ δ13C for carbonatites versus -5.7 to - 3.6 ‰ δ13C for kimberlites) require open-system fractionation at magmatic temperatures. Given that the oxidation state of Earth's mantle at >150 km depth is too reduced to enable larger volumes of 'pure' carbonate melt to migrate, it is reasonable to speculate that percolating near-solidus melts of carbonated peridotite must be silicate-dominated with only dilute carbonate contents, similar to the Tikiusaaq kimberlite compositions (e.g., 16-33 wt.% SiO2). This concept is supported by our findings from the North Atlantic craton where kimberlite and other deeply derived carbonated silicate melts, such as aillikites, exsolve their carbonate components within the shallow lithosphere en route to the Earth's surface, thereby producing carbonatite magmas. The relative abundances of trace elements of such highly

Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

Energy Technology Data Exchange (ETDEWEB)

Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

2007-02-21

Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

Preparation of Powdery Carbon Nanotwist and Application to Printed Field Emitter

Directory of Open Access Journals (Sweden)

Yuji Hosokawa

2007-01-01

Full Text Available In the present study, an automatic production system with sequencer control for the synthesis of carbon nanofibriform based on catalytic CVD using a substrate was developed. The carbon nanotwist (CNTw, which is one of the helical carbon nanofibers, was then synthesized in powdery form with an Ni–SnO2-composed catalyst. The production rate was 5 400 times that of the conventional CVD system and Ni–Cu–In2O3 catalyst. The powdery CNTw was easily scraped off the substrate, then pasted with organic binder, and printed by a squeegee method on ITO glass substrate for an electron field emitter. The field emission performance was found to be better than that of the directly grown CNTw film in conventional CVD with Ni–Cu catalyst.

Blind sequence-length estimation of low-SNR cyclostationary sequences

CSIR Research Space (South Africa)

Vlok, JD

2014-06-01

Full Text Available Several existing direct-sequence spread spectrum (DSSS) detection and estimation algorithms assume prior knowledge of the symbol period or sequence length, although very few sequence-length estimation techniques are available in the literature...

Raman spectroscopy as a tool to investigate the structure and electronic properties of carbon-atom wires

Directory of Open Access Journals (Sweden)

Alberto Milani

2015-02-01

Full Text Available Graphene, nanotubes and other carbon nanostructures have shown potential as candidates for advanced technological applications due to the different coordination of carbon atoms and to the possibility of π-conjugation. In this context, atomic-scale wires comprised of sp-hybridized carbon atoms represent ideal 1D systems to potentially downscale devices to the atomic level. Carbon-atom wires (CAWs can be arranged in two possible structures: a sequence of double bonds (cumulenes, resulting in a 1D metal, or an alternating sequence of single–triple bonds (polyynes, expected to show semiconducting properties. The electronic and optical properties of CAWs can be finely tuned by controlling the wire length (i.e., the number of carbon atoms and the type of termination (e.g., atom, molecular group or nanostructure. Although linear, sp-hybridized carbon systems are still considered elusive and unstable materials, a number of nanostructures consisting of sp-carbon wires have been produced and characterized to date. In this short review, we present the main CAW synthesis techniques and stabilization strategies and we discuss the current status of the understanding of their structural, electronic and vibrational properties with particular attention to how these properties are related to one another. We focus on the use of vibrational spectroscopy to provide information on the structural and electronic properties of the system (e.g., determination of wire length. Moreover, by employing Raman spectroscopy and surface enhanced Raman scattering in combination with the support of first principles calculations, we show that a detailed understanding of the charge transfer between CAWs and metal nanoparticles may open the possibility to tune the electronic structure from alternating to equalized bonds.

Molecular Characterization of a Dual Domain Carbonic Anhydrase From the Ctenidium of the Giant Clam, Tridacna squamosa, and Its Expression Levels After Light Exposure, Cellular Localization, and Possible Role in the Uptake of Exogenous Inorganic Carbon

Directory of Open Access Journals (Sweden)

Clarissa Z. Y. Koh

2018-03-01

Full Text Available A Dual-Domain Carbonic Anhydrase (DDCA had been sequenced and characterized from the ctenidia (gills of the giant clam, Tridacna squamosa, which lives in symbiosis with zooxanthellae. DDCA was expressed predominantly in the ctenidium. The complete cDNA coding sequence of DDCA from T. squamosa comprised 1,803 bp, encoding a protein of 601 amino acids and 66.7 kDa. The deduced DDCA sequence contained two distinct α-CA domains, each with a specific catalytic site. It had a high sequence similarity with tgCA from Tridacna gigas. In T. squamosa, the DDCA was localized apically in certain epithelial cells near the base of the ctenidial filament and the epithelial cells surrounding the tertiary water channels. Due to the presence of two transmembrane regions in the DDCA, one of the Zn2+-containing active sites could be located externally and the other one inside the cell. These results denote that the ctenidial DDCA was positioned to dehydrate HCO3- to CO2 in seawater, and to hydrate the CO2 that had permeated the apical membrane back to HCO3- in the cytoplasm. During insolation, the host clam needs to increase the uptake of inorganic carbon from the ambient seawater to benefit the symbiotic zooxanthellae; only then, can the symbionts conduct photosynthesis and share the photosynthates with the host. Indeed, the transcript and protein levels of DDCA/DDCA in the ctenidium of T. squamosa increased significantly after 6 and 12 h of exposure to light, respectively, denoting that DDCA could participate in the light-enhanced uptake and assimilation of exogenous inorganic carbon.

Occurrence of particle debris field during focused Ga ion beam milling of glassy carbon

Energy Technology Data Exchange (ETDEWEB)

Hu Qin [Centre for Industrial Photonics, Institute for Manufacturing, Department of Engineering, University of Cambridge, Alan Reece Building, 17 Charles Babbage Road, Cambridge, CB3 0FS (United Kingdom); O' Neill, William, E-mail: wo207@eng.cam.ac.uk [Centre for Industrial Photonics, Institute for Manufacturing, Department of Engineering, University of Cambridge, Alan Reece Building, 17 Charles Babbage Road, Cambridge, CB3 0FS (United Kingdom)

2010-08-01

To explore the machining characteristics of glassy carbon by focused ion beam (FIB), particles induced by FIB milling on glassy carbon have been studied in the current work. Nano-sized particles in the range of tens of nanometers up to 400 nm can often be found around the area subject to FIB milling. Two ion beam scanning modes - slow single scan and fast repetitive scan - have been tested. Fewer particles are found in single patterns milled in fast repetitive scan mode. For a group of test patterns milled in a sequence, it was found that a greater number of particles were deposited around sites machined early in the sequence. In situ EDX analysis of the particles showed that they were composed of C and Ga. The formation of particles is related to the debris generated at the surrounding areas, the low melting point of gallium used as FIB ion source and the high contact angle of gallium on glassy carbon induces de-wetting of Ga and the subsequent formation of Ga particles. Ultrasonic cleaning can remove over 98% of visible particles. The surface roughness (R{sub a}) of FIB milled areas after cleaning is less than 2 nm.

Occurrence of particle debris field during focused Ga ion beam milling of glassy carbon

International Nuclear Information System (INIS)

Hu Qin; O'Neill, William

2010-01-01

To explore the machining characteristics of glassy carbon by focused ion beam (FIB), particles induced by FIB milling on glassy carbon have been studied in the current work. Nano-sized particles in the range of tens of nanometers up to 400 nm can often be found around the area subject to FIB milling. Two ion beam scanning modes - slow single scan and fast repetitive scan - have been tested. Fewer particles are found in single patterns milled in fast repetitive scan mode. For a group of test patterns milled in a sequence, it was found that a greater number of particles were deposited around sites machined early in the sequence. In situ EDX analysis of the particles showed that they were composed of C and Ga. The formation of particles is related to the debris generated at the surrounding areas, the low melting point of gallium used as FIB ion source and the high contact angle of gallium on glassy carbon induces de-wetting of Ga and the subsequent formation of Ga particles. Ultrasonic cleaning can remove over 98% of visible particles. The surface roughness (R a ) of FIB milled areas after cleaning is less than 2 nm.

Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

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Kirkness Ewen

2006-10-01

Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

Sequence assembly

DEFF Research Database (Denmark)

Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

2009-01-01

Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

Science.gov (United States)

Tedersoo, Leho; Abarenkov, Kessy; Nilsson, R Henrik; Schüssler, Arthur; Grelet, Gwen-Aëlle; Kohout, Petr; Oja, Jane; Bonito, Gregory M; Veldre, Vilmar; Jairus, Teele; Ryberg, Martin; Larsson, Karl-Henrik; Kõljalg, Urmas

2011-01-01

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.

Carbon foam/hydroxyapatite coating for carbon/carbon composites: Microstructure and biocompatibility

Energy Technology Data Exchange (ETDEWEB)

Zhang, Leilei, E-mail: zhangleilei1121@aliyun.com; Li, Hejun; Li, Kezhi; Zhang, Shouyang; Lu, Jinhua; Li, Wei; Cao, Sheng; Wang, Bin

2013-12-01

To improve the surface biocompatibility of carbon/carbon composites, a carbon foam/hydroxyapatite coating was applied using a combination method of slurry procedure and ultrasound-assisted electrochemical deposition procedure. The morphology, microstructure and chemical composition of the coating were investigated by scanning electron microscopy, energy dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, Raman spectroscopy and X-ray diffraction. The biocompatibility of the carbon foam/hydroxyapatite coating was investigated by osteoblast-like MG63 cell culture tests. The results showed that the carbon foam could provide a large number of pores on the surface of carbon/carbon composites. The hydroxyapatite crystals could infiltrate into the pores and form the carbon foam/hydroxyapatite coating. The coating covered the carbon/carbon composites fully and uniformly with slice morphology. The cell response tests showed that the MG63 cells on carbon foam/hydroxyapatite coating had a better cell adhesion and cell proliferation than those on uncoated carbon/carbon composites. The carbon foam/hydroxyapatite coatings were cytocompatible and were beneficial to improve the biocompatibility. The approach presented here may be exploited for fabrication of carbon/carbon composite implant surfaces.

Carbon foam/hydroxyapatite coating for carbon/carbon composites: Microstructure and biocompatibility

International Nuclear Information System (INIS)

Zhang, Leilei; Li, Hejun; Li, Kezhi; Zhang, Shouyang; Lu, Jinhua; Li, Wei; Cao, Sheng; Wang, Bin

2013-01-01

To improve the surface biocompatibility of carbon/carbon composites, a carbon foam/hydroxyapatite coating was applied using a combination method of slurry procedure and ultrasound-assisted electrochemical deposition procedure. The morphology, microstructure and chemical composition of the coating were investigated by scanning electron microscopy, energy dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, Raman spectroscopy and X-ray diffraction. The biocompatibility of the carbon foam/hydroxyapatite coating was investigated by osteoblast-like MG63 cell culture tests. The results showed that the carbon foam could provide a large number of pores on the surface of carbon/carbon composites. The hydroxyapatite crystals could infiltrate into the pores and form the carbon foam/hydroxyapatite coating. The coating covered the carbon/carbon composites fully and uniformly with slice morphology. The cell response tests showed that the MG63 cells on carbon foam/hydroxyapatite coating had a better cell adhesion and cell proliferation than those on uncoated carbon/carbon composites. The carbon foam/hydroxyapatite coatings were cytocompatible and were beneficial to improve the biocompatibility. The approach presented here may be exploited for fabrication of carbon/carbon composite implant surfaces.

Influence of the stacking sequence of layers on the mechanical behavior of polymeric composite cylinders

International Nuclear Information System (INIS)

Carvalho, Osni de

2006-01-01

This work evaluated experimentally the influence of the stacking sequence of layers symmetrical and asymmetrical on the mechanical behavior of polymeric composite cylinders. For so much, two open-ended cylinders groups were manufactured by filament winding process, which had different stacking sequence related to the laminate midplane, characterizing symmetrical and asymmetrical laminates. The composite cylinders were made with epoxy matrix and carbon fiber as reinforcement. For evaluation of the mechanical strength, the cylinders were tested hydrostatically, which consisted of internal pressurization in a hydrostatic device through the utilization of a fluid until the cylinders burst. Additionally, were compared the strains and failure modes between the cylinders groups. The utilization of a finite element program allowed to conclude that this tool, very used in design, does not get to identify tensions in the fiber direction in each composite layer, as well as interlaminar shear stress, that appears in the cylinders with asymmetrical stacking sequence. The tests results showed that the stacking sequence had influence in the mechanical behavior of the composite cylinders, favoring the symmetrical construction. (author)

Complete genome sequence of Halanaerobium praevalens type strain (GSLT)

Energy Technology Data Exchange (ETDEWEB)

Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Chertkov, Olga [Los Alamos National Laboratory (LANL); Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kannan, K. Palani [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute

2011-01-01

Halanaerobium praevalens Zeikus et al. 1984 is the type species of the genus Halanaero- bium, which in turn is the type genus of the family Halanaerobiaceae. The species is of inter- est because it is able to reduce a variety of nitro-substituted aromatic compounds at a high rate, and because of its ability to degrade organic pollutants. The strain is also of interest be- cause it functions as a hydrolytic bacterium, fermenting complex organic matter and produc- ing intermediary metabolites for other trophic groups such as sulfate-reducing and methano- genic bacteria. It is further reported as being involved in carbon removal in the Great Salt Lake, its source of isolation. This is the first completed genome sequence of a representative of the genus Halanaerobium and the second genome sequence from a type strain of the fami- ly Halanaerobiaceae. The 2,309,262 bp long genome with its 2,110 protein-coding and 70 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Shotgun protein sequencing.

Energy Technology Data Exchange (ETDEWEB)

Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

2009-06-01

A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

Characterization and classification of one new cytoplasmic male sterility (CMS) line based on morphological, cytological and molecular markers in non-heading Chinese cabbage (Brassica rapa L.).

Science.gov (United States)

Heng, Shuangping; Shi, Dianyi; Hu, Zhenhua; Huang, Tao; Li, Jinping; Liu, Liyan; Xia, Chunxiu; Yuan, Zhenzhen; Xu, Yuejin; Fu, Tingdong; Wan, Zhengjie

2015-09-01

A new non-heading Chinese cabbage CMS line M119A was characterized and specific molecular markers were developed to classify different CMS types. One new non-heading Chinese cabbage (Brassica rapa L.) cytoplasmic male sterile (CMS) line M119A was obtained by interspecific crosses between the recently discovered hau CMS line of Brassica juncea and B. rapa. Furthermore, the line was characterized and compared with other five isonuclear-alloplasmic CMS lines. The M119A line produced six stamens without pollen and only two stamen fused together in fewer flowers. Tissue section indicated that anther abortion in M119A may have occurred during differentiation of the archesporial cells without pollen sac. All the six CMS lines were grouped into three types based on the presence of three PCR fragments of 825, 465 and 772 bp amplified with different mitochondrial genes specific primers. The 825-bp fragment was amplified both in 09-10A and H201A using the specific primer pair P-orf224-atp6, and showed 100 % identity with the mitochondrial gene of pol CMS. The 465-bp fragment was amplified in 30A and 105A using the primer pair P-orf138 and shared 100 % identity with the mitochondrial gene of ogu CMS. The 772-bp fragment was amplified in M119A and H203A using the primer pair P-orf288 and showed 100 % identity with the mitochondrial gene of hau CMS. Therefore, these markers could efficiently distinguish different types of isonuclear-alloplasmic CMS lines of non-heading Chinese cabbage, which were useful for improving the efficiency of cross-breeding and heterosis utilization in cruciferous vegetables.

Foundations of Sequence-to-Sequence Modeling for Time Series

OpenAIRE

Kuznetsov, Vitaly; Mariet, Zelda

2018-01-01

The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...

Diffusion-weighted MR imaging findings in carbon monoxide poisoning

International Nuclear Information System (INIS)

Teksam, M.; Casey, S.O.; Michel, E.; Liu, H.; Truwit, C.L.

2002-01-01

Diffusion-weighted MR imaging (DWI) of two patients with carbon monoxide (CO) poisoning demonstrated white matter and cortical hyperintensities. In one patient, the changes on the FLAIR sequence were more subtle than those on DWI. The DWI abnormality in this patient represented true restriction. In the second patient, repeated exposure to CO caused restricted diffusion. DWI may be helpful for earlier identification of the changes of acute CO poisoning. (orig.)

Characterization and expression of the maize β-carbonic anhydrase gene repeat regions.

Science.gov (United States)

Tems, Ursula; Burnell, James N

2010-12-01

In maize, carbonic anhydrase (CA; EC 4.2.1.1) catalyzes the first reaction of the C(4) photosynthetic pathway; it catalyzes the hydration of CO(2) to bicarbonate and provides an inorganic carbon source for the primary carboxylation reaction catalyzed by phosphoenolpyruvate (PEP) carboxylase. The β-CA isozymes from maize, as well as other agronomically important NADP-malic enzyme (NADP-ME) type C(4) crops, have remained relatively uncharacterized but differ significantly from the β-CAs of other C(4) monocot species primarily due to transcript length and the presence of repeat sequences. This research confirmed earlier findings of repeat sequences in maize CA transcripts, and demonstrated that the gene encoding these transcripts is also composed of repeat sequences. One of the maize CA genes was sequenced and found to encode two domains, with distinct groups of exons corresponding to the repeat regions of the transcript. We have also shown that expression of a single repeat region of the CA transcript produced active enzyme that associated as a dimer and was composed primarily of α-helices, consistent with that observed for other plant CAs. As the presence of repeat regions in the CA gene is unique to NADP-ME type C(4) monocot species, the implications of these findings in the context of the evolution of the location and function of this C(4) pathway enzyme are strongly suggestive of CA gene duplication resulting in an evolutionary advantage and a higher photosynthetic efficiency. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

Detection of M-Sequences from Spike Sequence in Neuronal Networks

Directory of Open Access Journals (Sweden)

Yoshi Nishitani

2012-01-01

Full Text Available In circuit theory, it is well known that a linear feedback shift register (LFSR circuit generates pseudorandom bit sequences (PRBS, including an M-sequence with the maximum period of length. In this study, we tried to detect M-sequences known as a pseudorandom sequence generated by the LFSR circuit from time series patterns of stimulated action potentials. Stimulated action potentials were recorded from dissociated cultures of hippocampal neurons grown on a multielectrode array. We could find several M-sequences from a 3-stage LFSR circuit (M3. These results show the possibility of assembling LFSR circuits or its equivalent ones in a neuronal network. However, since the M3 pattern was composed of only four spike intervals, the possibility of an accidental detection was not zero. Then, we detected M-sequences from random spike sequences which were not generated from an LFSR circuit and compare the result with the number of M-sequences from the originally observed raster data. As a result, a significant difference was confirmed: a greater number of “0–1” reversed the 3-stage M-sequences occurred than would have accidentally be detected. This result suggests that some LFSR equivalent circuits are assembled in neuronal networks.

Genome Sequencing

DEFF Research Database (Denmark)

Sato, Shusei; Andersen, Stig Uggerhøj

2014-01-01

The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

Fatigue life prediction in woven carbon fabric polyester composites

International Nuclear Information System (INIS)

Khan, Z.; Al-Sulaiman, F.S.; Farooqi, J.K.

1999-01-01

An analytical model, based on stiffness degradation during fatigue loading, which has been used for fatigue life predictions in the Fiber Reinforced Plastics (FRP), is employed to examine its validity to the fatigue life predictions in the Woven Fabric Reinforced Plastics. The rate of stiffness degradation (dE/dN) has been obtained from the constant amplitude fatigue testing of 8-ply coupons made from prepreg plain-weave woven carbon-carbon fabric having a polyester resin as the matrix material. The test coupons had three different ply stacking sequences, namely, the unidirectional (0)8,and two off axis plied (0,0,+45,-45)s, and (+45,-45,0,0)s orientations. The estimated fatigue lives obtained from the damage rate function dD/dN, which in turn was a function of the stiffness degradation rate dE/dN, were compared with the experimentally observed fatigue life data. It is shown that the stiffness degradation model provides reasonably good correlation between the analytically determined fatigue lives and the experimentally observed fatigue for the plain-weave woven Carbon-Carbon Fabric Reinforced Plastic Composites. (author)

Potential role of multiple carbon fixation pathways during lipid accumulation in Phaeodactylum tricornutum

Directory of Open Access Journals (Sweden)

Valenzuela Jacob

2012-06-01

Full Text Available Abstract Background Phaeodactylum tricornutum is a unicellular diatom in the class Bacillariophyceae. The full genome has been sequenced (P. tricornutum gene expression profiles during nutrient-deprivation and lipid-accumulation, cell cultures were grown with a nitrate to phosphate ratio of 20:1 (N:P and whole-genome transcripts were monitored over time via RNA-sequence determination. Results The specific Nile Red (NR fluorescence (NR fluorescence per cell increased over time; however, the increase in NR fluorescence was initiated before external nitrate was completely exhausted. Exogenous phosphate was depleted before nitrate, and these results indicated that the depletion of exogenous phosphate might be an early trigger for lipid accumulation that is magnified upon nitrate depletion. As expected, many of the genes associated with nitrate and phosphate utilization were up-expressed. The diatom-specific cyclins cyc7 and cyc10 were down-expressed during the nutrient-deplete state, and cyclin B1 was up-expressed during lipid-accumulation after growth cessation. While many of the genes associated with the C3 pathway for photosynthetic carbon reduction were not significantly altered, genes involved in a putative C4 pathway for photosynthetic carbon assimilation were up-expressed as the cells depleted nitrate, phosphate, and exogenous dissolved inorganic carbon (DIC levels. P. tricornutum has multiple, putative carbonic anhydrases, but only two were significantly up-expressed (2-fold and 4-fold at the last time point when exogenous DIC levels had increased after the cessation of growth. Alternative pathways that could utilize HCO3- were also suggested by the gene expression profiles (e.g., putative propionyl-CoA and methylmalonyl-CoA decarboxylases. Conclusions The results indicate that P. tricornutum continued carbon dioxide reduction when population growth was arrested and different carbon-concentrating mechanisms were used dependent upon exogenous

[Complete genome sequencing and sequence analysis of BCG Tice].

Science.gov (United States)

Wang, Zhiming; Pan, Yuanlong; Wu, Jun; Zhu, Baoli

2012-10-04

The objective of this study is to obtain the complete genome sequence of Bacillus Calmette-Guerin Tice (BCG Tice), in order to provide more information about the molecular biology of BCG Tice and design more reasonable vaccines to prevent tuberculosis. We assembled the data from high-throughput sequencing with SOAPdenovo software, with many contigs and scaffolds obtained. There are many sequence gaps and physical gaps remained as a result of regional low coverage and low quality. We designed primers at the end of contigs and performed PCR amplification in order to link these contigs and scaffolds. With various enzymes to perform PCR amplification, adjustment of PCR reaction conditions, and combined with clone construction to sequence, all the gaps were finished. We obtained the complete genome sequence of BCG Tice and submitted it to GenBank of National Center for Biotechnology Information (NCBI). The genome of BCG Tice is 4334064 base pairs in length, with GC content 65.65%. The problems and strategies during the finishing step of BCG Tice sequencing are illuminated here, with the hope of affording some experience to those who are involved in the finishing step of genome sequencing. The microarray data were verified by our results.

Transcriptome sequencing and whole genome expression profiling of chrysanthemum under dehydration stress

Science.gov (United States)

2013-01-01

Background Chrysanthemum is one of the most important ornamental crops in the world and drought stress seriously limits its production and distribution. In order to generate a functional genomics resource and obtain a deeper understanding of the molecular mechanisms regarding chrysanthemum responses to dehydration stress, we performed large-scale transcriptome sequencing of chrysanthemum plants under dehydration stress using the Illumina sequencing technology. Results Two cDNA libraries constructed from mRNAs of control and dehydration-treated seedlings were sequenced by Illumina technology. A total of more than 100 million reads were generated and de novo assembled into 98,180 unique transcripts which were further extensively annotated by comparing their sequencing to different protein databases. Biochemical pathways were predicted from these transcript sequences. Furthermore, we performed gene expression profiling analysis upon dehydration treatment in chrysanthemum and identified 8,558 dehydration-responsive unique transcripts, including 307 transcription factors and 229 protein kinases and many well-known stress responsive genes. Gene ontology (GO) term enrichment and biochemical pathway analyses showed that dehydration stress caused changes in hormone response, secondary and amino acid metabolism, and light and photoperiod response. These findings suggest that drought tolerance of chrysanthemum plants may be related to the regulation of hormone biosynthesis and signaling, reduction of oxidative damage, stabilization of cell proteins and structures, and maintenance of energy and carbon supply. Conclusions Our transcriptome sequences can provide a valuable resource for chrysanthemum breeding and research and novel insights into chrysanthemum responses to dehydration stress and offer candidate genes or markers that can be used to guide future studies attempting to breed drought tolerant chrysanthemum cultivars. PMID:24074255

Water circulation control on carbonate-δ18O records in a low permeability clay formation and surrounding limestones: The Upper Dogger-Oxfordian sequence from the eastern Paris basin, France

International Nuclear Information System (INIS)

Lavastre, Veronique; Ader, Magali; Buschaert, Stephane; Petit, Eddy; Javoy, Marc

2011-01-01

Research highlights: → Up. Dog./Oxf. sequence is investigated for radioactive waste disposal feasibilities. → Marine carbonates suffered isotopic exchanges with meteoric water. → Modelling shows that very low W/R ratio can explain isotopic changes in clay layer. → Higher W/R ratio are needed to reach isotopic changes in carbonated layers. → Confirmed barrier property of clay layer was probably reached during early burial. - Abstract: Upper Dogger to Oxfordian Formations in the eastern part of the Paris basin (France) are currently being investigated by the French nuclear waste management agency (Andra), testing the feasibility of long-term deep nuclear waste disposal in the Callovo-Oxfordian claystones. Characterising the hydrogeological behaviour of the Callovo-Oxfordian claystones is, therefore, essential in evaluating its potential as a geological barrier. In order to evaluate and quantify water/rock interactions experienced over geological time by these Formations, bulk carbonate δ 13 C and δ 18 O were measured and calculations of water-rock ratios were used to explain carbonate-δ 18 O changes. Meteoric porewater and a maximum temperature reached of about 40 deg. C were considered. The Jurassic marine carbonate δ 13 C was preserved in the Callovo-Oxfordian claystones and in the overlying limestones (-0.28 per mille to 3.39 per mille/PDB), while the δ 18 O values are lower by 0-5 per mille (-6.25 per mille to -1.32 per mille/PDB). Calculations show that Upper Dogger and Oxfordian Limestone δ 18 O data: (i)have random-like distribution through theoretical δ 18 O-W/R curves and (ii)suggest that water/rock ratios (0.08-0.4) needed to explain δ 18 O changes are higher by a factor of about 2-20 compared to the present-day water/rock ratio. These features indicate advection in both aquifers. According to the history of the Paris basin, this hydrogeological behaviour could have been effective since Jurassic/Cretaceous transition times. Inversely, the

Genotoxicity of carbon nanofibers: Are they potentially more or less dangerous than carbon nanotubes or asbestos?

International Nuclear Information System (INIS)

Kisin, E.R.; Murray, A.R.; Sargent, L.; Lowry, D.; Chirila, M.; Siegrist, K.J.; Schwegler-Berry, D.; Leonard, S.; Castranova, V.; Fadeel, B.; Kagan, V.E.; Shvedova, A.A.

2011-01-01

The production of carbon nanofibers and nanotubes (CNF/CNT) and their composite products is increasing globally. CNF are generating great interest in industrial sectors such as energy production and electronics, where alternative materials may have limited performance or are produced at a much higher cost. However, despite the increasing industrial use of carbon nanofibers, information on their potential adverse health effects is limited. In the current study, we examine the cytotoxic and genotoxic potential of carbon-based nanofibers (Pyrograf (registered) -III) and compare this material with the effects of asbestos fibers (crocidolite) or single-walled carbon nanotubes (SWCNT). The genotoxic effects in the lung fibroblast (V79) cell line were examined using two complementary assays: the comet assay and micronucleus (MN) test. In addition, we utilized fluorescence in situ hybridization to detect the chromatin pan-centromeric signals within the MN indicating their origin by aneugenic (chromosomal malsegregation) or clastogenic (chromosome breakage) mechanisms. Cytotoxicity tests revealed a concentration- and time-dependent loss of V79 cell viability after exposure to all tested materials in the following sequence: asbestos > CNF > SWCNT. Additionally, cellular uptake and generation of oxygen radicals was seen in the murine RAW264.7 macrophages following exposure to CNF or asbestos but not after administration of SWCNT. DNA damage and MN induction were found after exposure to all tested materials with the strongest effect seen for CNF. Finally, we demonstrated that CNF induced predominately centromere-positive MN in primary human small airway epithelial cells (SAEC) indicating aneugenic events. Further investigations are warranted to elucidate the possible mechanisms involved in CNF-induced genotoxicity.

Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

Science.gov (United States)

de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

2000-01-01

Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

Metagenomic insight into methanogenic reactors promoting direct interspecies electron transfer via granular activated carbon.

Science.gov (United States)

Park, Jeong-Hoon; Park, Jong-Hun; Je Seong, Hoon; Sul, Woo Jun; Jin, Kang-Hyun; Park, Hee-Deung

2018-07-01

To provide insight into direct interspecies electron transfer via granular activated carbon (GAC), the effect of GAC supplementation on anaerobic digestion was evaluated. Compared to control samples, the GAC supplementation increased the total amount of methane production and its production rate by 31% and 72%, respectively. 16S rDNA sequencing analysis revealed a shift in the archaeal community composition; the Methanosarcina proportion decreased 17%, while the Methanosaeta proportion increased 5.6%. Metagenomic analyses based on shotgun sequencing demonstrated that the abundance of pilA and omcS genes belonging to Geobacter species decreased 69.4% and 29.4%, respectively. Furthermore, the analyses suggested a carbon dioxide reduction pathway rather than an acetate decarboxylation pathway for methane formation. Taken together, these results suggest that GAC improved methane production performance by shifting the microbial community and altering functional genes associated with direct interspecies electron transfer via conductive materials. Copyright © 2018 Elsevier Ltd. All rights reserved.

Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

Directory of Open Access Journals (Sweden)

Jian eWu

2012-11-01

Full Text Available Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome.

Correlating carbon and oxygen isotope events in early to middle Miocene shallow marine carbonates in the Mediterranean region using orbitally tuned chemostratigraphy and lithostratigraphy

Science.gov (United States)

Auer, Gerald; Piller, Werner E.; Reuter, Markus; Harzhauser, Mathias

2015-04-01

During the Miocene prominent oxygen isotope events (Mi-events) reflect major changes in glaciation, while carbonate isotope maxima (CM-events) reflect changes in organic carbon burial, particularly during the Monterey carbon isotope excursion. However, despite their importance to the global climate history they have never been recorded in shallow marine carbonate successions. The Decontra section on the Maiella Platform (central Apennines, Italy), however, allows to resolve them for the first time in such a setting during the early to middle Miocene. The present study improves the stratigraphic resolution of parts of the Decontra section via orbital tuning of high-resolution gamma ray (GR) and magnetic susceptibility data to the 405 kyr eccentricity metronome. The tuning allows, within the established biostratigraphic, sequence stratigraphic, and isotope stratigraphic frameworks, a precise correlation of the Decontra section with pelagic records of the Mediterranean region, as well as the global paleoclimatic record and the global sea level curve. Spectral series analyses of GR data further indicate that the 405 kyr orbital cycle is particularly well preserved during the Monterey Event. Since GR is a direct proxy for authigenic uranium precipitation during increased burial of organic carbon in the Decontra section, it follows the same long-term orbital pacing as observed in the carbon isotope records. The 405 kyr GR beat is thus correlated with the carbon isotope maxima observed during the Monterey Event. Finally, the Mi-events can now be recognized in the δ18O record and coincide with plankton-rich, siliceous, or phosphatic horizons in the lithology of the section.

Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T)

Energy Technology Data Exchange (ETDEWEB)

Han, Cliff; Spring, Stefan; Lapidus, Alla; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C.; Saunders, Elizabeth; Chertkov, Olga; Brettin, Thomas; Goker, Markus; Rohde, Manfred; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Detter, John C.

2009-05-20

Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phylum 'Bacteroidetes'. P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several enzymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Sequence Algebra, Sequence Decision Diagrams and Dynamic Fault Trees

International Nuclear Information System (INIS)

Rauzy, Antoine B.

2011-01-01

A large attention has been focused on the Dynamic Fault Trees in the past few years. By adding new gates to static (regular) Fault Trees, Dynamic Fault Trees aim to take into account dependencies among events. Merle et al. proposed recently an algebraic framework to give a formal interpretation to these gates. In this article, we extend Merle et al.'s work by adopting a slightly different perspective. We introduce Sequence Algebras that can be seen as Algebras of Basic Events, representing failures of non-repairable components. We show how to interpret Dynamic Fault Trees within this framework. Finally, we propose a new data structure to encode sets of sequences of Basic Events: Sequence Decision Diagrams. Sequence Decision Diagrams are very much inspired from Minato's Zero-Suppressed Binary Decision Diagrams. We show that all operations of Sequence Algebras can be performed on this data structure.

Four-electron deoxygenative reductive coupling of carbon monoxide at a single metal site

Science.gov (United States)

Buss, Joshua A.; Agapie, Theodor

2016-01-01

Carbon dioxide is the ultimate source of the fossil fuels that are both central to modern life and problematic: their use increases atmospheric levels of greenhouse gases, and their availability is geopolitically constrained. Using carbon dioxide as a feedstock to produce synthetic fuels might, in principle, alleviate these concerns. Although many homogeneous and heterogeneous catalysts convert carbon dioxide to carbon monoxide, further deoxygenative coupling of carbon monoxide to generate useful multicarbon products is challenging. Molybdenum and vanadium nitrogenases are capable of converting carbon monoxide into hydrocarbons under mild conditions, using discrete electron and proton sources. Electrocatalytic reduction of carbon monoxide on copper catalysts also uses a combination of electrons and protons, while the industrial Fischer-Tropsch process uses dihydrogen as a combined source of electrons and electrophiles for carbon monoxide coupling at high temperatures and pressures. However, these enzymatic and heterogeneous systems are difficult to probe mechanistically. Molecular catalysts have been studied extensively to investigate the elementary steps by which carbon monoxide is deoxygenated and coupled, but a single metal site that can efficiently induce the required scission of carbon-oxygen bonds and generate carbon-carbon bonds has not yet been documented. Here we describe a molybdenum compound, supported by a terphenyl-diphosphine ligand, that activates and cleaves the strong carbon-oxygen bond of carbon monoxide, enacts carbon-carbon coupling, and spontaneously dissociates the resulting fragment. This complex four-electron transformation is enabled by the terphenyl-diphosphine ligand, which acts as an electron reservoir and exhibits the coordinative flexibility needed to stabilize the different intermediates involved in the overall reaction sequence. We anticipate that these design elements might help in the development of efficient catalysts for

Subsurface Permian reef complexes of southern Tunisia: Shelf carbonate setting and paleogeographic implications

Science.gov (United States)

Zaafouri, Adel; Haddad, Sofiene; Mannaî-Tayech, Beya

2017-05-01

2-D seismic reflection sections, borehole data as well as published and unpublished data have been investigated to reconstruct the paleogeography of southern Tunisia during Middle to Late Permian times. Paleogeographical reconstruction based on the integration of petroleum well data and 2-D seismic facies interpretation shows three main depositional areas with very contrasting sedimentary pile. These are 1) a subsiding basin; 2) an outer shelf carbonate, and 3) an inner shelf carbonate. Based on typical electric responses of reef buildups to seismic wave, we shall urge that during Middle Permian times, the outer carbonate shelf was subject of reef barrier development. Lithology evidences from core samples show that reef framework correspond mainly to fossiliferous limestone and dolomite. The WNW-ESE recognized reef barrier led between latitudes 33° 10‧ 00″N and 33° 20‧ 00″N. The Tebaga of Medenine outcrop constitutes the northern-edge of this barrier. Westward it may be extended to Bir Soltane area whereas its extension eastward is still to be determined. Biogenic buildups took place preferentially over faulted Carboniferous and lower Paleozoic paleohighs resulting likely from the Hercynian orogeny. The subsiding basin is located north of Tebaga of Medenine outcrop where Upper Permian sedimentary sequence is made entirely of 4000 m deep marine green silty shale facies. These are ascribed to unorganized and chaotic reflectors. Inner carbonate shelf facies succession corresponds to a typical interbedding of shallow marine carbonate deposits, shale, dolomite, and anhydrite inducing parallel-layered of strong amplitude and good continuity reflectors. Also within the inner carbonate shelf patch reef or reef pinnacles have been identified based on their seismic signature particularly their low vertical development as compared to reef complexes. Southward, towards Sidi Toui area, the Upper Permian depositional sequence thins out and bears witness of land

Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform

Directory of Open Access Journals (Sweden)

Shan Wei

2018-05-01

Full Text Available Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples’ genomic DNA in under three hours, including library preparation and sequencing. This novel method shows great promise as a clinical diagnostic test for applications requiring rapid short-read DNA sequencing.

Magnetic susceptibility evolution and sedimentary environments on carbonate platform sediments and atolls, comparison of the Frasnian from Belgium and Alberta, Canada

Science.gov (United States)

da Silva, Anne-Christine; Potma, Ken; Weissenberger, John A. W.; Whalen, Michael T.; Humblet, Marc; Mabille, Cédric; Boulvain, Frédéric

2009-02-01

Magnetic susceptibility (MS) measurements on carbonate rocks are considered as a proxy for impurities delivered to the carbonate environments. In the absence of strong climatic or tectonic variations, bulk MS values have been linked to sea level variations, because sea-level fall increases clastic supply and therefore increases in magnetic mineral deposition. In this paper we explore the relationship between the average magnitude of bulk MS, with shallowing-up sequences and facies evolution in different Devonian carbonate complexes. Similarities and differences between these parameters have been scrutinized in carbonate attached platform and detached platforms (mounds and/or atolls) from Belgium and Canada. In the carbonate attached platforms from Belgium and Canada, the MS patterns are directly related to depositional environment. Mean MS values increase from the most distal towards the most proximal facies and towards the top of the majority of fourth-order shallowing-up sequences. These trends are in agreement with theoretical background (MS increases with regression). In the Belgian detached platform, the average MS pattern generally shows an opposite behaviour to that observed in the attached carbonate platforms. Average MS decreases towards the most proximal facies and towards the top of a majority of the fourth-order shallowing-up sequences. This behaviour can be explained by the influence of sedimentary rate and water agitation during deposition. A high sedimentary rate will dilute the magnetic minerals in the atoll facies and the high water agitation during deposition may be expected to have prevented the deposition of the magnetic grains. So, the combination of these two effects will result in the observed low values in the atoll crown and lagoonal facies. In the Canadian detached platform, MS is mainly negative. This means that the limestones are very pure. The technique does not appear to be appropriate in these rocks. The variations of average MS

Complete genome sequence of Rhodospirillum rubrum type strain (S1).

Science.gov (United States)

Munk, A Christine; Copeland, Alex; Lucas, Susan; Lapidus, Alla; Del Rio, Tijana Glavina; Barry, Kerrie; Detter, John C; Hammon, Nancy; Israni, Sanjay; Pitluck, Sam; Brettin, Thomas; Bruce, David; Han, Cliff; Tapia, Roxanne; Gilna, Paul; Schmutz, Jeremy; Larimer, Frank; Land, Miriam; Kyrpides, Nikos C; Mavromatis, Konstantinos; Richardson, Paul; Rohde, Manfred; Göker, Markus; Klenk, Hans-Peter; Zhang, Yaoping; Roberts, Gary P; Reslewic, Susan; Schwartz, David C

2011-07-01

Rhodospirillum rubrum (Esmarch 1887) Molisch 1907 is the type species of the genus Rhodospirillum, which is the type genus of the family Rhodospirillaceae in the class Alphaproteobacteria. The species is of special interest because it is an anoxygenic phototroph that produces extracellular elemental sulfur (instead of oxygen) while harvesting light. It contains one of the most simple photosynthetic systems currently known, lacking light harvesting complex 2. Strain S1(T) can grow on carbon monoxide as sole energy source. With currently over 1,750 PubMed entries, R. rubrum is one of the most intensively studied microbial species, in particular for physiological and genetic studies. Next to R. centenum strain SW, the genome sequence of strain S1(T) is only the second genome of a member of the genus Rhodospirillum to be published, but the first type strain genome from the genus. The 4,352,825 bp long chromosome and 53,732 bp plasmid with a total of 3,850 protein-coding and 83 RNA genes were sequenced as part of the DOE Joint Genome Institute Program DOEM 2002.

Accommodation and supply—a dual control on stratigraphic sequences

Science.gov (United States)

Schlager, Wolfgang

1993-07-01

It is widely accepted that both eustatic and tectonically controlled regional changes of sea level have contributed to the record of stratigraphic sequences. I suggest that environmental change be added as a third, autonomous control. Sedimentologic principles clearly indicate that sequences and their systems tracts are controlled by the interplay of two rates —the rate of change in accommodation (space available for sedimentation) and the rate of sediment supply. Sea level has direct control on accommodation, but its influence on sediment supply is remote and easily overshadowed by environmental factors. For instance, the record of the most recent sea-level rise is a transgressive systems tract where supply is low; it is a prograding highstand systems tract in deltas where the supply is high. Examples of sequence boundaries generated by changes in sediment supply include tectonically driven shifts in sediment input into basins, changes in ocean currents, pulsating supply from failure of submarine slopes and drowning of carbonate platforms by environmental stress. Furthermore, the stratigraphic sequences in fluviatile continental basins are physically removed from sea-level induced changes in accommodation and must have formed by changes in the rate and pattern of supply. Subaerial exposure of marine sediments at the sequence boundary is a most important criterion for recognizing sea level cycles as opposed to supply cycles. Other criteria include downstepping of shelf breaks and characteristic patterns in the spacing of time lines within sequences. Some third-order cycles (ca. 0.5-3 Ma duration) meet these criteria, others do not. Cycle-stacking patterns and the shifting facies belts on cratons indicate that many second- and third-order cycles lack pronounced exposure unconformities and represent gradual changes superimposed on more rapid, shorter oscillations. Seismic data yield poor images of these gradational changes because they lack resolution. Seismic

Genome sequence of a microbial lipid producing fungus Cryptococcus albidus NT2002.

Science.gov (United States)

Yong, Xiaoyu; Yan, Zhiying; Xu, Lin; Zhou, Jun; Wu, Xiayuan; Wu, Yuandong; Li, Yang; Chen, Zugeng; Zhou, Hua; Wei, Ping; Jia, Honghua

2016-04-10

Cryptococcus albidus NT2002, isolated from the soil in Xinjiang, China, appeared to have the ability to accumulate microbial lipid by utilizing various carbon sources. The predominant properties make it as a potential bio-platform for biodiesel production. Here, we report the complete genome sequence of C. albidus NT2002, which might provide a basis for further elucidation of the genetic background of this promising strain for developing metabolic engineering strategies to produce biodiesel in a green and sustainable manner. Copyright © 2016 Elsevier B.V. All rights reserved.

Carbon-On-Carbon Manufacturing

Science.gov (United States)

Mungas, Gregory S. (Inventor); Buchanan, Larry (Inventor); Banzon, Jr., Jose T. (Inventor)

2017-01-01

The presently disclosed technology relates to carbon-on-carbon (C/C) manufacturing techniques and the resulting C/C products. One aspect of the manufacturing techniques disclosed herein utilizes two distinct curing operations that occur at different times and/or using different temperatures. The resulting C/C products are substantially non-porous, even though the curing operation(s) substantially gasify a liquid carbon-entrained filler material that saturates a carbon fabric that makes up the C/C products.

Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

Directory of Open Access Journals (Sweden)

Joern Toedling

Full Text Available Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.

[Carbon storage of forest stands in Shandong Province estimated by forestry inventory data].

Science.gov (United States)

Li, Shi-Mei; Yang, Chuan-Qiang; Wang, Hong-Nian; Ge, Li-Qiang

2014-08-01

Based on the 7th forestry inventory data of Shandong Province, this paper estimated the carbon storage and carbon density of forest stands, and analyzed their distribution characteristics according to dominant tree species, age groups and forest category using the volume-derived biomass method and average-biomass method. In 2007, the total carbon storage of the forest stands was 25. 27 Tg, of which the coniferous forests, mixed conifer broad-leaved forests, and broad-leaved forests accounted for 8.6%, 2.0% and 89.4%, respectively. The carbon storage of forest age groups followed the sequence of young forests > middle-aged forests > mature forests > near-mature forests > over-mature forests. The carbon storage of young forests and middle-aged forests accounted for 69.3% of the total carbon storage. Timber forest, non-timber product forest and protection forests accounted for 37.1%, 36.3% and 24.8% of the total carbon storage, respectively. The average carbon density of forest stands in Shandong Province was 10.59 t x hm(-2), which was lower than the national average level. This phenomenon was attributed to the imperfect structure of forest types and age groups, i. e., the notably higher percentage of timber forests and non-timber product forest and the excessively higher percentage of young forests and middle-aged forest than mature forests.

Carbon steel protection in G.S. (Girlder sulfide) plants. CITROSOLV process influence. Pt. 6

International Nuclear Information System (INIS)

Lires, O.A.; Burkart, A.L.; Delfino, C.A.; Rojo, E.A.

1988-01-01

In order to protect carbon steel towers and piping of Girlder sulfide (G.S.) experimental heavy water plants against corrosion produced by the action of aqueous solutions of hydrogen sulfides, a method, previously published, was developed. Carbon steel, exposed to saturated aqueous solutions of hydrogen sulfide, forms iron sulfide scales. In oxygen free solutions evolution of corrosion follows the sequence: mackinawite → cubic ferrous sulfide → troilite → pyrrotite → pyrite. Scales formed by pyrrotite-pyrite or pyrite are the most protective layers (these are obtained at 130 deg C, 2 MPa, for periods of 14 days). CITROSOLV Process (Pfizer) is used to descaling and passivating stainless steel plant's components. This process must be used in mixed (carbon steel - stainless steel) circuits and may cause the formation of magnetite scales over the carbon steel. The influence of magnetite in the pyrrotite-pyrite scales formation is studied in this work. (Author) [es

Water circulation control on carbonate-{delta}{sup 18}O records in a low permeability clay formation and surrounding limestones: The Upper Dogger-Oxfordian sequence from the eastern Paris basin, France

Energy Technology Data Exchange (ETDEWEB)

Lavastre, Veronique, E-mail: veronique.lavastre@univ-st-etienne.fr [Universite de Lyon, Universite Jean Monnet, F-42023 Saint Etienne (France)] [CNRS, UMR 6524, LMV, F-42023 Saint Etienne (France)] [Laboratoire de Geochimie des Isotopes Stables, Institut de Physique du Globe de Paris and Universite Paris 7 - UMR CNRS 7154, 4, place Jussieu, 75252 Paris cedex 05 (France); Ader, Magali [Laboratoire de Geochimie des Isotopes Stables, Institut de Physique du Globe de Paris and Universite Paris 7 - UMR CNRS 7154, 4, place Jussieu, 75252 Paris cedex 05 (France); Buschaert, Stephane [Andra, Parc de la Croix Blanche, 7-8 rue Jean Monnet, 92 298 Chatenay-Malabry Cedex (France); Petit, Eddy; Javoy, Marc [Laboratoire de Geochimie des Isotopes Stables, Institut de Physique du Globe de Paris and Universite Paris 7 - UMR CNRS 7154, 4, place Jussieu, 75252 Paris cedex 05 (France)

2011-05-15

Research Highlights: > Up. Dog./Oxf. sequence is investigated for radioactive waste disposal feasibilities. > Marine carbonates suffered isotopic exchanges with meteoric water. > Modelling shows that very low W/R ratio can explain isotopic changes in clay layer. > Higher W/R ratio are needed to reach isotopic changes in carbonated layers. > Confirmed barrier property of clay layer was probably reached during early burial. - Abstract: Upper Dogger to Oxfordian Formations in the eastern part of the Paris basin (France) are currently being investigated by the French nuclear waste management agency (Andra), testing the feasibility of long-term deep nuclear waste disposal in the Callovo-Oxfordian claystones. Characterising the hydrogeological behaviour of the Callovo-Oxfordian claystones is, therefore, essential in evaluating its potential as a geological barrier. In order to evaluate and quantify water/rock interactions experienced over geological time by these Formations, bulk carbonate {delta}{sup 13}C and {delta}{sup 18}O were measured and calculations of water-rock ratios were used to explain carbonate-{delta}{sup 18}O changes. Meteoric porewater and a maximum temperature reached of about 40 deg. C were considered. The Jurassic marine carbonate {delta}{sup 13}C was preserved in the Callovo-Oxfordian claystones and in the overlying limestones (-0.28 per mille to 3.39 per mille/PDB), while the {delta}{sup 18}O values are lower by 0-5 per mille (-6.25 per mille to -1.32 per mille/PDB). Calculations show that Upper Dogger and Oxfordian Limestone {delta}{sup 18}O data: (i)have random-like distribution through theoretical {delta}{sup 18}O-W/R curves and (ii)suggest that water/rock ratios (0.08-0.4) needed to explain {delta}{sup 18}O changes are higher by a factor of about 2-20 compared to the present-day water/rock ratio. These features indicate advection in both aquifers. According to the history of the Paris basin, this hydrogeological behaviour could have been

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.

Carbonate hosted gold deposit in Tasmania, Australia

International Nuclear Information System (INIS)

Abadi, M.H.

1999-01-01

Full text: This study uses elemental and isotopic composition of carbonates associated with gold from Henty and Beaconsfield in Tasmania, Australia, to illustrate source of gold-bearing fluids, salinity, temperature and dissolution and reprecipitation of carbonate. The Beaconsfield and Henty gold mines are located in northern and western Tasmania respectively. Gold mineralisation in Beaconsfield occurs within the quartz-carbonate Tasmania Reef (Lower to Middle Palaeozoic sequence, Hills, 1998). The Henty gold mine is located at the base of the Cambrian Tyndall Group (volcano-sedimentary succession, White and McPhie, 1996) close to Henty Fault. Gold in carbonate samples from Henty ranges from 7.7 to 9360 ppm and in Beaconsfield ranges from 0.01 to 434 ppm. The amount of carbonate in samples from Henty and Beaconsfield gold mines varies from approximately 24 to 99.8%. Bivariate plot of Ca relative to total amounts of Mg, Fe and Mn illustrates that the major carbonate minerals at Beaconsfield and Henty gold mines are magnesian ankerite and calcite. The difference in carbonate mineralogy, at Henty and Beaconsfield gold mines, is attributed to the composition of fluids responsible for carbonate alteration. Gold and magnesium in Beaconsfield ankerite are derived from the leaching of Cambrian ultramafic rocks during the Devonian by the passage of meteoric fluids through tectonically affected Ordovician carbonates (Rao and Adabi, 1999). The total concentration of Fe and Mn are low (0.5 to 2%) in Henty and high (1 to 17.5%) in Beaconsfield ankerite, possibly due to oxidising conditions at Henty and reducing conditions at Beaconsfield gold mines during gold mineralisation. Variation of Sr values between Beaconsfield ankerite and Henty calcite is related to dissolution of limestone that increase Sr concentrations in gold mineralising fluids. Na values in both Beaconsfield (20 to 1100 ppm) and Henty carbonates (25 to 1650 ppm) suggest low salinity fluids responsible for gold

Water-table and discharge changes associated with the 2016-2017 seismic sequence in central Italy: hydrogeological data and a conceptual model for fractured carbonate aquifers

Science.gov (United States)

Petitta, Marco; Mastrorillo, Lucia; Preziosi, Elisabetta; Banzato, Francesca; Barberio, Marino Domenico; Billi, Andrea; Cambi, Costanza; De Luca, Gaetano; Di Carlo, Giuseppe; Di Curzio, Diego; Di Salvo, Cristina; Nanni, Torquato; Palpacelli, Stefano; Rusi, Sergio; Saroli, Michele; Tallini, Marco; Tazioli, Alberto; Valigi, Daniela; Vivalda, Paola; Doglioni, Carlo

2018-01-01

A seismic sequence in central Italy from August 2016 to January 2017 affected groundwater dynamics in fractured carbonate aquifers. Changes in spring discharge, water-table position, and streamflow were recorded for several months following nine Mw 5.0-6.5 seismic events. Data from 22 measurement sites, located within 100 km of the epicentral zones, were analyzed. The intensity of the induced changes were correlated with seismic magnitude and distance to epicenters. The additional post-seismic discharge from rivers and springs was found to be higher than 9 m3/s, totaling more than 0.1 km3 of groundwater release over 6 months. This huge and unexpected contribution increased streamflow in narrow mountainous valleys to previously unmeasured peak values. Analogously to the L'Aquila 2009 post-earthquake phenomenon, these hydrogeological changes might reflect an increase of bulk hydraulic conductivity at the aquifer scale, which would increase hydraulic heads in the discharge zones and lower them in some recharge areas. The observed changes may also be partly due to other mechanisms, such as shaking and/or squeezing effects related to intense subsidence in the core of the affected area, where effects had maximum extent, or breaching of hydraulic barriers.

Relative influence of deposition and diagenesis on carbonate reservoir layering

Energy Technology Data Exchange (ETDEWEB)

Poli, Emmanuelle [Total E and P, Courbevoie (France); Javaux, Catherine [Total E and P, Pointe Noire (Congo)

2008-07-01

The architecture heterogeneities and petrophysical properties of carbonate reservoirs result from a combination of platform morphology, related depositional environments, relative sea level changes and diagenetic events. The reservoir layering built for static and dynamic modelling purposes should reflect the key heterogeneities (depositional or diagenetic) which govern the fluid flow patterns. The layering needs to be adapted to the goal of the modelling, ranging from full field computations of hydrocarbon volumes, to sector-based fine-scale simulations to test the recovery improvement. This paper illustrates various reservoir layering types, including schemes dominated by depositional architecture, and those more driven by the diagenetic overprint. The examples include carbonate platform reservoirs from different stratigraphic settings (Tertiary, Cretaceous, Jurassic and Permian) and different regions (Europe, Africa and Middle East areas). This review shows how significant stratigraphic surfaces (such as sequence boundaries or maximum flooding) with their associated facies shifts, can be often considered as key markers to constrain the reservoir layering. Conversely, how diagenesis (dolomitization and karst development), resulting in units with particular poroperm characteristics, may significantly overprint the primary reservoir architecture by generating flow units which cross-cut depositional sequences. To demonstrate how diagenetic processes can create reservoir bodies with geometries that cross-cut the depositional fabric, different types of dolomitization and karst development are illustrated. (author)

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

DEFF Research Database (Denmark)

Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

2012-01-01

Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS...

Carbons and carbon supported catalysts in hydroprocessing

Energy Technology Data Exchange (ETDEWEB)

Furimsky, Edward

2009-07-01

This book is a comprehensive summary of recent research in the field and covers all areas of carbons and carbon materials. The potential application of carbon supports, particularly those of carbon black (CB) and activated carbon (AC) in hydroprocessing catalysis are covered. Novel carbon materials such as carbon fibers and carbon nano tubes (CNT) are also covered, including the more recent developments in the use of fullerenes in hydroprocessing applications. Although the primary focus of this book is on carbons and carbon supported catalysts, it also identifies the difference in the effect of carbon supports compared with the oxidic supports, particularly that of the Al{sub 2}O{sub 3}. The difference in catalyst activity and stability was estimated using both model compounds and real feeds under variable conditions. The conditions applied during the preparation of carbon supported catalysts are also comprehensively covered and include various methods of pretreatment of carbon supports to enhance catalyst performance. The model compounds results consistently show higher hydrodesulfurization and hydrodeoxygenation activities of carbon supported catalysts than that of the Al{sub 2}O{sub 3} supported catalysts. Also, the deactivation of the former catalysts by coke deposition was much less evident. Chapter 6.3.1.3 is on carbon-supported catalysts: coal-derived liquids.

Disentangling the control of tectonics, eustasy, trophic conditions and climate on shallow-marine carbonate production during the Aalenian-Oxfordian interval: From the western France platform to the western Tethyan domain

Science.gov (United States)

Andrieu, Simon; Brigaud, Benjamin; Barbarand, Jocelyn; Lasseur, Eric; Saucède, Thomas

2016-11-01

The objective of this work is to improve our understanding of the processes controlling changes in the architecture and facies of intracontinental carbonate platforms. We examined the facies and sequence stratigraphy of Aalenian to Oxfordian limestones of western France. Seventy-seven outcrop sections were studied and thirty-one sedimentary facies identified in five depositional environments ranging from lower offshore to backshore. Platform evolution was reconstructed along a 500 km cross-section. Twenty-two depositional sequences were identified on the entire western France platform and correlated with European third-order sequences at the biozone level, demonstrating that eustasy was the major factor controlling the cyclic trend of accommodation. The tectonic subsidence rate was computed from accommodation measurements from the Aalenian to the Oxfordian in key localities. Tectonism controlled the sedimentation rate and platform architecture at a longer time scale. Tectonic subsidence triggered the demise of carbonate production at the Bathonian/Callovian boundary while the uplift made possible the recovery of carbonate platform from Caen to Le Mans during the mid Oxfordian. Topography of the Paleozoic basement mainly controlled lateral variations of paleodepth within the western France platform until the mid Bathonian. A synthesis of carbonate production in the western Tethyan domain at that time was conducted. Stages of high carbonate production during the Bajocian/Bathonian and the middle to late Oxfordian are synchronous with low δ13C, high eccentricity intervals, and rather dry climate promoting (1) evaporation and carbonate supersaturation, and (2) oligotrophic conditions. Periods of low carbonate production during the Aalenian and from the middle Callovian to early Oxfordian correlate with high δ13C and low eccentricity intervals, characterized by wet climate and less oligotrophic conditions. Such conditions tend to diminish growth potential of carbonate

Roles of repetitive sequences

Energy Technology Data Exchange (ETDEWEB)

Bell, G.I.

1991-12-31

The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

Some aspects of the development of the Vaal Reef uranium-gold carbon seams, Witwatersrand sequence: organic geochemical and microbiological considerations

International Nuclear Information System (INIS)

Zumberge, J.E.; Nagy, B.; Nagy, L.A.

1981-01-01

The solvent-insoluble organic matter (kerogen) that is the predominant syngenetic component of the Vaal Reef carbon seams was analyzed by combined high-vacuum pyrolysis gas-chromatography mass spectrometry, combined electron microprobe-scanning electron microscopy and electron paramagnetic resonance spectroscopy. The pyrolysis results indicate that the Vaal Reef carbon is a random polymer-type matter consisting mainly of aromatic and short-chain aliphatic hydrocarbons, as well as aromatic and other organic-sulfur constituents. Scanning electron microscopy revealed coccoid and filamentous microstructures in the carbonaceous seams. These structures are conceivably of biological affinity and may be fossil blue-green algae and (or) bacteria. Gold is often concentrated at the interfaces of admixed clay-carbon microenvironments. This implies physical and chemical interactions between clays and organic matter conducive to the entrapment of detrital gold during deposition and the crystallization of colloidal/dissolved gold in the carbon seams. High concentrations of organic free radicals (molecules with unpaired electrons) in the carbonaceous matter, deduced from electron paramagnetic resonance spectroscopy, suggest that radiation emitted from uranium played a unique role in the reconstitution and polymerization of the progenitor biochemicals

Deep-Water Resedimented Carbonate Exploration Play Types: Controls and Models

Science.gov (United States)

Minzoni, M.; Janson, X.; Kerans, C.; Playton, T.; Winefield, P.; Burgess, P. M.

2016-12-01

Deepwater resedimented deposits have been described in both modern and ancient carbonate sequences, many with good reservoir potential, for example the giant Cretaceous Poza Rica field in Mexico ( 40 MMBoe), the Mississippian Tangiz field in Kazakhstan, and several fields in the U.S. Permian basin (several Tcf gas). Nevertheless, carbonate slope and basin systems remain poorly understood when compared to their siliciclastic counterparts. Legacy published and unpublished work, combined with a global database of surface and sub-surface examples of resedimented carbonates, has highlighted that downslope resedimentation of carbonate material is in large part controlled by the evolution of the parent platform margin, which in turn is best characterized in terms of various controlling processes such as the carbonate factory type, tectonic setting, eustatic variations, and prevailing wind direction and ocean current patterns. Two generic play types emerge: (i) attached carbonate slope play -developed immediately adjacent to the parent carbonate platform and dominated by rock fall and platform collapse deposits or in situ boundstone; and (ii) detached carbonate slope play - deposited further from the platform margin via channelized turbidity currents and other mass-flow processes. High-rising, steep, bypass platform margins with collapse scars and grain-dominated factories have the highest potential to generate channelized and detached deep-water reservoirs with high initial porosity and permeability. Best reservoirs are aragonitic grainstones transported from the platform into the adjacent basin, and undergoing dissolution in submarine undersaturated water with early formation of secondary porosity to further enhance reservoir properties. Any exploration model aiming at identifying potential resedimented carbonate plays should be based on carbonate platform configurations and factory types favorable for re-sedimentation of large sedimentary bodies and preservation or

Probabilistic Motor Sequence Yields Greater Offline and Less Online Learning than Fixed Sequence.

Science.gov (United States)

Du, Yue; Prashad, Shikha; Schoenbrun, Ilana; Clark, Jane E

2016-01-01

It is well acknowledged that motor sequences can be learned quickly through online learning. Subsequently, the initial acquisition of a motor sequence is boosted or consolidated by offline learning. However, little is known whether offline learning can drive the fast learning of motor sequences (i.e., initial sequence learning in the first training session). To examine offline learning in the fast learning stage, we asked four groups of young adults to perform the serial reaction time (SRT) task with either a fixed or probabilistic sequence and with or without preliminary knowledge (PK) of the presence of a sequence. The sequence and PK were manipulated to emphasize either procedural (probabilistic sequence; no preliminary knowledge (NPK)) or declarative (fixed sequence; with PK) memory that were found to either facilitate or inhibit offline learning. In the SRT task, there were six learning blocks with a 2 min break between each consecutive block. Throughout the session, stimuli followed the same fixed or probabilistic pattern except in Block 5, in which stimuli appeared in a random order. We found that PK facilitated the learning of a fixed sequence, but not a probabilistic sequence. In addition to overall learning measured by the mean reaction time (RT), we examined the progressive changes in RT within and between blocks (i.e., online and offline learning, respectively). It was found that the two groups who performed the fixed sequence, regardless of PK, showed greater online learning than the other two groups who performed the probabilistic sequence. The groups who performed the probabilistic sequence, regardless of PK, did not display online learning, as indicated by a decline in performance within the learning blocks. However, they did demonstrate remarkably greater offline improvement in RT, which suggests that they are learning the probabilistic sequence offline. These results suggest that in the SRT task, the fast acquisition of a motor sequence is driven

Nonparametric combinatorial sequence models.

Science.gov (United States)

Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

2011-11-01

This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer.

Science.gov (United States)

Wang, Ji; Ke, Yue Hua; Zhang, Yong; Huang, Ke Qiang; Wang, Lei; Shen, Xin Xin; Dong, Xiao Ping; Xu, Wen Bo; Ma, Xue Jun

2017-10-01

Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Within the first minute (min) of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min (on average), 99% identity was achieved for 10 CA16 strains in a single run. MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use. Copyright © 2017 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

The relationship between carbonate facies, volcanic rocks and plant remains in a late Palaeozoic lacustrine system (San Ignacio Fm, Frontal Cordillera, San Juan province, Argentina)

Science.gov (United States)

Busquets, P.; Méndez-Bedia, I.; Gallastegui, G.; Colombo, F.; Cardó, R.; Limarino, O.; Heredia, N.; Césari, S. N.

2013-07-01

The San Ignacio Fm, a late Palaeozoic foreland basin succession that crops out in the Frontal Cordillera (Argentinean Andes), contains lacustrine microbial carbonates and volcanic rocks. Modification by extensive pedogenic processes contributed to the massive aspect of the calcareous beds. Most of the volcanic deposits in the San Ignacio Fm consist of pyroclastic rocks and resedimented volcaniclastic deposits. Less frequent lava flows produced during effusive eruptions led to the generation of tabular layers of fine-grained, greenish or grey andesites, trachytes and dacites. Pyroclastic flow deposits correspond mainly to welded ignimbrites made up of former glassy pyroclasts devitrified to microcrystalline groundmass, scarce crystals of euhedral plagioclase, quartz and K-feldspar, opaque minerals, aggregates of fine-grained phyllosilicates and fiammes defining a bedding-parallel foliation generated by welding or diagenetic compaction. Widespread silicified and silica-permineralized plant remains and carbonate mud clasts are found, usually embedded within the ignimbrites. The carbonate sequences are underlain and overlain by volcanic rocks. The carbonate sequence bottoms are mostly gradational, while their tops are usually sharp. The lower part of the carbonate sequences is made up of mud which appear progressively, filling interstices in the top of the underlying volcanic rocks. They gradually become more abundant until they form the whole of the rock fabric. Carbonate on volcanic sandstones and pyroclastic deposits occur, with the nucleation of micritic carbonate and associated production of pyrite. Cyanobacteria, which formed the locus of mineral precipitation, were related with this nucleation. The growth of some of the algal mounds was halted by the progressive accumulation of volcanic ash particles, but in most cases the upper boundary is sharp and suddenly truncated by pyroclastic flows or volcanic avalanches. These pyroclastic flows partially destroyed the

The microbially mediated soil organic carbon loss under degenerative succession in an alpine meadow.

Science.gov (United States)

Zhang, Yuguang; Liu, Xiao; Cong, Jing; Lu, Hui; Sheng, Yuyu; Wang, Xiulei; Li, Diqiang; Liu, Xueduan; Yin, Huaqun; Zhou, Jizhong; Deng, Ye

2017-07-01

Land-cover change has long been recognized as having marked effect on the amount of soil organic carbon (SOC). However, the microbially mediated processes and mechanisms on SOC are still unclear. In this study, the soil samples in a degenerative succession from alpine meadow to alpine steppe meadow in the Qinghai-Tibetan Plateau were analysed using high-throughput technologies, including Illumina sequencing and geochip functional gene arrays. The soil microbial community structure and diversity were significantly (p carbon degradation genes (e.g., pectin and hemicellulose) was significantly higher in alpine steppe meadow than in alpine meadow, but the relative abundance of soil recalcitrant carbon degradation genes (e.g., chitin and lignin) showed the opposite tendency. The Biolog Ecoplate experiment showed that microbially mediated soil carbon utilization was more active in alpine steppe meadow than in alpine meadow. Consequently, more soil labile carbon might be decomposed in alpine steppe meadow than in alpine meadow. Therefore, the degenerative succession of alpine meadow because of climate change or anthropogenic activities would most likely decrease SOC and nutrients medicated by changing soil microbial community structure and their functional potentials for carbon decomposition. © 2017 John Wiley & Sons Ltd.

Transcriptome-based analysis on carbon metabolism of Haematococcus pluvialis mutant under 15% CO2.

Science.gov (United States)

Li, Ke; Cheng, Jun; Lu, Hongxiang; Yang, Weijuan; Zhou, Junhu; Cen, Kefa

2017-06-01

To elucidate the mechanism underlying the enhanced growth rate in the Haematococcus pluvialis mutated with 60 Co-γ rays and domesticated with 15% CO 2 , transcriptome sequencing was conducted to clarify the carbon metabolic pathways of mutant cells. The CO 2 fixation rate of mutant cells increased to 2.57gL -1 d -1 under 15% CO 2 due to the enhanced photosynthesis, carbon fixation, glycolysis pathways. The upregulation of PetH, ATPF0A and PetJ related to photosynthetic electron transport, ATP synthase and NADPH generation promoted the photosynthesis. The upregulation of genes related to Calvin cycle and ppdK promoted carbon fixation in both C3 and C4 photosynthetic pathways. The reallocation of carbon was also enhanced under 15% CO 2 . The 19-, 14- and 3.5-fold upregulation of FBA, TPI and PK genes, respectively, remarkably promoted the glycolysis pathways. This accelerated the conversion of photosynthetic carbon to pyruvate, which was an essential precursor for astaxanthin and lipids biosynthesis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Carbon steel protection in G.S. [Girldler sulphide] plants: Pt. 7

International Nuclear Information System (INIS)

Lires, Osvaldo; Delfino, Cristina; Rojo, Enrique.

1989-01-01

In order to protect carbon steel towers and piping of a GS experimental heavy water plant against corrosion produced by the action of aqueous solutions of hydrogen sulphide, a method, elsewhere published, was developed. Carbon steel exposed to saturated aqueous solutions of hydrogen sulphide forms iron sulphide scales. In oxygen free solutions, evolution of corrosion follows the sequence mackinawite → cubic ferrous sulphide → troilite → pyrrotite → pyrite. Scales formed by pyrrotite and pyrite are the most protective layers (these are obtained at 130 deg C, 2 MPa for a period of 14 days). During a plant shutdown procedures, the carbon steel protected with those scales is exposed to water and highly humid air; under such conditions oxidation is unavoidable. Later, treatment in plant conditions does not regenerate scales because the composition of regenerated scales involves more soluble iron sulphides such as mackinawite and troilite. Therefore, it is not recommendable to expose the protective scales to atmospherical conditions. (Author)

Carbon/Carbon Pistons for Internal Combustion Engines

Science.gov (United States)

Taylor, A. H.

1986-01-01

Carbon/carbon piston performs same function as aluminum pistons in reciprocating internal combustion engines while reducing weight and increasing mechanical and thermal efficiencies of engine. Carbon/carbon piston concept features low piston-to-cylinder wall clearance - so low piston rings and skirts unnecessary. Advantages possible by negligible coefficient of thermal expansion of carbon/carbon.

Architecture and evolution of an Early Permian carbonate complex on a tectonically active island in east-central California

Science.gov (United States)

Stevens, Calvin H.; Magginetti, Robert T.; Stone, Paul

2015-01-01

The newly named Upland Valley Limestone represents a carbonate complex that developed on and adjacent to a tectonically active island in east-central California during a brief interval of Early Permian (late Artinskian) time. This lithologically unique, relatively thin limestone unit lies within a thick sequence of predominantly siliciclastic rocks and is characterized by its high concentration of crinoidal debris, pronounced lateral changes in thickness and lithofacies, and a largely endemic fusulinid fauna. Most outcrops represent a carbonate platform and debris derived from it and shed downslope, but another group of outcrops represents one or possibly more isolated carbonate buildups that developed offshore from the platform. Tectonic activity in the area occurred before, probably during, and after deposition of this short-lived carbonate complex.

Geochemical variations during the 2012 Emilia seismic sequence

Science.gov (United States)

Sciarra, Alessandra; Cantucci, Barbara; Galli, Gianfranco; Cinti, Daniele; Pizzino, Luca

2015-04-01

Several geochemical surveys (soil gas and shallow water) were performed in the Modena province (Massa Finalese, Finale Emilia, Medolla and S. Felice sul Panaro), during 2006-2014 period. In May-June 2012, a seismic sequence (main shocks of ML 5.9 and 5.8) was occurred closely to the investigated area. In this area 300 CO2 and CH4 fluxes measurements, 150 soil gas concentrations (He, H2, CO2, CH4 and C2H6), 30 shallow waters and their isotopic analyses (δ13C- CH4, δD- CH4 and δ13C- CO2) were performed in April-May 2006, October and December 2008, repeated in May and September 2012, June 2013 and July 2014 afterwards the 2012 Emilia seismic sequences. Chemical composition of soil gas are dominated by CH4 in the southern part by CO2 in the northern part. Very anomalous fluxes and concentrations are recorded in spot areas; elsewhere CO2 and CH4 values are very low, within the typical range of vegetative and of organic exhalation of the cultivated soil. After the seismic sequence the CH4 and CO2 fluxes are increased of one order of magnitude in the spotty areas, whereas in the surrounding area the values are within the background. On the contrary, CH4 concentration decrease (40%v/v in the 2012 surveys) and CO2 concentration increase until to 12.7%v/v (2013 survey). Isotopic gas analysis were carried out only on samples with anomalous values. Pre-seismic data hint a thermogenic origin of CH4 probably linked to leakage from a deep source in the Medolla area. Conversely, 2012/2013 isotopic data indicate a typical biogenic origin (i.e. microbial hydrocarbon production) of the CH4, as recognized elsewhere in the Po Plain and surroundings. The δ13C-CO2 value suggests a prevalent shallow origin of CO2 (i.e. organic and/or soil-derived) probably related to anaerobic oxidation of heavy hydrocarbons. Water samples, collected from domestic, industrial and hydrocarbons exploration wells, allowed us to recognize different families of waters. Waters are meteoric in origin and

Carbon dioxide conversion over carbon-based nanocatalysts.

Science.gov (United States)

Khavarian, Mehrnoush; Chai, Siang-Piao; Mohamed, Abdul Rahman

2013-07-01

The utilization of carbon dioxide for the production of valuable chemicals via catalysts is one of the efficient ways to mitigate the greenhouse gases in the atmosphere. It is known that the carbon dioxide conversion and product yields are still low even if the reaction is operated at high pressure and temperature. The carbon dioxide utilization and conversion provides many challenges in exploring new concepts and opportunities for development of unique catalysts for the purpose of activating the carbon dioxide molecules. In this paper, the role of carbon-based nanocatalysts in the hydrogenation of carbon dioxide and direct synthesis of dimethyl carbonate from carbon dioxide and methanol are reviewed. The current catalytic results obtained with different carbon-based nanocatalysts systems are presented and how these materials contribute to the carbon dioxide conversion is explained. In addition, different strategies and preparation methods of nanometallic catalysts on various carbon supports are described to optimize the dispersion of metal nanoparticles and catalytic activity.

Changes in the thermoelectric response of vitreous carbon due to the irradiation by γ-rays

Science.gov (United States)

Culebras, M.; Madroñero, A.; Mota, C.; Gómez, C. M.; Amo, Jose M.; Cantarero, A.

2014-07-01

In order to study variations in the thermoelectric properties, some commercial glassy carbon samples were subjected to a sequence of steps consisting of a combination of irradiation with γ-rays produced by radioisotopes 60Co, and hydrogen adsorption when the samples were put in an over pressured atmosphere of this gas. With this procedure it was possible to observe that the irradiation decreases the electrical conductivity of glassy carbon samples and the hydrogenation changes the sign of Seebeck coefficient. The material initially is an n-type semiconductor, but with hydrogenation changes to p-type semiconductor. X-ray diffraction analysis showed that the hydrogenated vitreous carbon is more amorphous than the pristine material and the γ-rays irradiation produces changes in the crystallite size and shape.

Organic carbon degradation in arctic marine sediments, Svalbard: A comparison of initial and terminal steps

DEFF Research Database (Denmark)

Arnosti, C.; Jørgensen, BB

2006-01-01

carbohydrate concentrations were comparable to those measured in more temperate sediments, and likely comprise a considerable fraction of porewater dissolved organic carbon. A comparison of dissolved carbohydrate inventories with hydrolysis and sulfate reduction rates suggests that the turnover of carbon......Degradation of marine organic matter under anoxic conditions involves microbial communities working in concert to remineralize complex substrates to CO2. In order to investigate the coupling between the initial and terminal steps of this sequence in permanently cold sediments, rates...... of extracellular enzymatic hydrolysis and sulfate reduction were measured in parallel cores collected from 5 fjords on the west and northwest coast of Svalbard, in the high Arctic. Inventories of total dissolved carbohydrates were also measured in order to evaluate their potential role in carbon turnover...

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

Directory of Open Access Journals (Sweden)

Baldwin Stephen A

2011-03-01

Full Text Available Abstract Background Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. Results The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. Conclusions PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.

Science.gov (United States)

Troshin, Peter V; Postis, Vincent Lg; Ashworth, Denise; Baldwin, Stephen A; McPherson, Michael J; Barton, Geoffrey J

2011-03-07

Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

Cathode spot movements along the carbon fibres in carbon/carbon composites

International Nuclear Information System (INIS)

Zhang Chengyu; Qiao Shengru; Yang Zhimao; Ding Bingjun

2007-01-01

The cathode spot movements on a polyacrilonitrile (PAN)-based carbon felt reinforced C/C composite and a three dimensional PAN-based carbon fibre reinforced C/C composite (3D-C/C) were investigated by a scanning electron microscope and a digital high-speed video camera. It was found that the carbon fibres have a higher ability to withstand the vacuum arc erosion than the carbon matrix. The cathode spot walks on the matrix, rather than on the carbon fibres. The cathode spot motion is controlled by the architecture of carbon fibres in C/C. The cathode spots move along the carbon fibres by a step-by-step manner rather than a random walk. The cathode spot tracks spread over a wide zone on the 3D-C/C surface parallel to the carbon fibre. The average arc spreading velocity is estimated to be about 0.9 m s -1 and the transient arc spreading velocity is in the range of 0.54-4.5 m s -1

Radiation damage in carbon-carbon composites

International Nuclear Information System (INIS)

Burchell, T.D.; Eartherly, W.P.; Nelson, G.E.

1992-01-01

Graphite and carbon-carbon composite materials are widely used in plasma facing applications in current Tokamak devices such as TFTR and DIIID in the USA, JET, Tore Supra and TEXTOR in Europe, and JT-60U in Japan. Carbon-carbon composites are attractive choices for Tokamak limiters and diverters because of their low atomic number, high thermal shock resistance, high melting point, and high thermal conductivity. Next generation machines such as the International Thermonuclear Experimental Reactor (ITER) will utilize carbon-carbon composites in their first wall and diverter. ITER will be an ignition machine and thus will produce substantial neutron fluences from the D-T fusion reaction. The resultant high energy neutrons will cause carbon atom displacements in the plasma facing materials which will markedly affect their structure and physical properties. The effect of neutron damage on graphite has been studied for over forty years. Recently the effects of neutron irradiation on the fusion relevant graphite GraphNOL N3M was reviewed. In contrast to graphite, relatively little work has been performed to elucidate the effects of neutron irradiation on carbon-carbon composites. The results of our previous irradiation experiments have been published elsewhere. Here the irradiation induced dimensional changes in 1D, 2D, and 3D carbon-carbon composites are reported for fluences up to 4.7 dpa at an irradiation temperature of 600 degree C

Sequence embedding for fast construction of guide trees for multiple sequence alignment

LENUS (Irish Health Repository)

Blackshields, Gordon

2010-05-14

Abstract Background The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences. This requires memory and time proportional to N 2 for N sequences. When N grows larger than 10,000 or so, this becomes increasingly prohibitive and can form a significant barrier to carrying out very large multiple alignments. Results In this paper, we have tested variations on a class of embedding methods that have been designed for clustering large numbers of complex objects where the individual distance calculations are expensive. These methods involve embedding the sequences in a space where the similarities within a set of sequences can be closely approximated without having to compute all pair-wise distances. Conclusions We show how this approach greatly reduces computation time and memory requirements for clustering large numbers of sequences and demonstrate the quality of the clusterings by benchmarking them as guide trees for multiple alignment. Source code is available for download from http:\\/\\/www.clustal.org\\/mbed.tgz.

Two-step carbon coating of lithium vanadium phosphate as high-rate cathode for lithium-ion batteries

Science.gov (United States)

Kuang, Quan; Zhao, Yanming

2012-10-01

Carbon-coated Li3V2(PO4)3 was firstly prepared at 850 °C via two-step reaction method combined sol-gel and conventional solid-state synthesis by using VPO4/carbon as an intermediate. Two different carbon sources, citric acid and glucose as carbon additives in sequence, ultimately deduced double carbon-coated Li3V2(PO4)3 as a high-rate cathode material. The Li3V2(PO4)3/carbon with 4.39% residual carbon has a splendid electronic conductivity of 4.76×10-2 S cm-1. Even in the voltage window of 2.5-4.8 V, the Li3V2(PO4)3/carbon cathode can retain outstanding rate ability (170.4 mAh g-1 at 1.2 C, 101.9 mAh g-1 at 17 C), and no degradation is found after 120 C current rate. These phenomena show that the two-step carbon-coated Li3V2(PO4)3 can act as a fast charge-discharge cathode material for high-power Li-ion batteries. Furthermore, it's believed that this synthesize method can be easily transplanted to prepare other lithiated vanadium-based phosphates.

Sequencing of BAC pools by different next generation sequencing platforms and strategies

Directory of Open Access Journals (Sweden)

Scholz Uwe

2011-10-01

Full Text Available Abstract Background Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs improve the assemblies by scaffolding and whether barcoding of BACs is dispensable. Results Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library. Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%. Conclusion Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.

Identification and characterization of a novel zebrafish (Danio rerio pentraxin–carbonic anhydrase

Directory of Open Access Journals (Sweden)

Maarit S. Patrikainen

2017-12-01

Full Text Available Background Carbonic anhydrases (CAs are ubiquitous, essential enzymes which catalyze the conversion of carbon dioxide and water to bicarbonate and H+ ions. Vertebrate genomes generally contain gene loci for 15–21 different CA isoforms, three of which are enzymatically inactive. CA VI is the only secretory protein of the enzymatically active isoforms. We discovered that non-mammalian CA VI contains a C-terminal pentraxin (PTX domain, a novel combination for both CAs and PTXs. Methods We isolated and sequenced zebrafish (Danio rerio CA VI cDNA, complete with the sequence coding for the PTX domain, and produced the recombinant CA VI–PTX protein. Enzymatic activity and kinetic parameters were measured with a stopped-flow instrument. Mass spectrometry, analytical gel filtration and dynamic light scattering were used for biophysical characterization. Sequence analyses and Bayesian phylogenetics were used in generating hypotheses of protein structure and CA VI gene evolution. A CA VI–PTX antiserum was produced, and the expression of CA VI protein was studied by immunohistochemistry. A knock-down zebrafish model was constructed, and larvae were observed up to five days post-fertilization (dpf. The expression of ca6 mRNA was quantitated by qRT-PCR in different developmental times in morphant and wild-type larvae and in different adult fish tissues. Finally, the swimming behavior of the morphant fish was compared to that of wild-type fish. Results The recombinant enzyme has a very high carbonate dehydratase activity. Sequencing confirms a 530-residue protein identical to one of the predicted proteins in the Ensembl database (ensembl.org. The protein is pentameric in solution, as studied by gel filtration and light scattering, presumably joined by the PTX domains. Mass spectrometry confirms the predicted signal peptide cleavage and disulfides, and N-glycosylation in two of the four observed glycosylation motifs. Molecular modeling of the pentamer is

Relative age and age sequence of fractions of soil organic matter

International Nuclear Information System (INIS)

Scharpenseel, H.W.

1975-01-01

Natural radiocarbon measurements on soil fractions provide information regarding the chances of separating the ''old biologically inert carbon'' out of samples of recent soil material. Beyond this, the relative fraction ages are scrutinized for the sequential order of the origin of the fractions within the biosynthetic reaction chain of soil humic matter. Among all fractions compared (classic humic matter fractionation by alkali and acid treatment; successive extraction with organic solvents of increasing polarity; separation according to particle size by Sephadex gel filtration; hydrolysis residue) the 6 n HCl hydrolysis residue shows the most consistent significant age increment. Repeated exhaustive hydrolysis treatment of the same sample material is still pending. All other fraction types indicate an age pattern under strong predetermination by method of origin, e.g., existence or lack of hydromorphy, without an evident enrichment of the ''old biologically inert carbon''. Among the organic extracts, no persistent age hierarchy is noticeable, whereas the classical fractions follow an age sequence mainly parallel to an increase of the molecular weight. Hymatomelanic acids appear rejuvenated by relics of recent carbon derived from the extractant ethanol. Grey humic acids are older than the brown humic acids, humines from fully terrestrial soil environment are older than humic acids, while in hydromorphic soils, cold alkali insoluble young C-compounds seem to be conserved which are liable to falsify rejuvenation of the humines

Long sequence correlation coprocessor

Science.gov (United States)

Gage, Douglas W.

1994-09-01

A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

Next-Generation Sequencing Platforms

Science.gov (United States)

Mardis, Elaine R.

2013-06-01

Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

Optimization of sequence alignment for simple sequence repeat regions

Directory of Open Access Journals (Sweden)

Ogbonnaya Francis C

2011-07-01

Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

Analyses of the Sn IX-Sn XII spectra in the EUV region

International Nuclear Information System (INIS)

Churilov, S S; Ryabtsev, A N

2006-01-01

The Sn IX-Sn XII spectra excited in a vacuum spark have been analysed in the 130-160 A wavelength region. The analysis was based on the energy parameter extrapolation in the isonuclear Sn VI-VIII and Sn XIII-XIV sequence. 266 spectral lines belonging to the 4d m -(4d m-1 4f+4p 5 4d m+1 ) (m=6-3) transition arrays were classified in the Sn IX-Sn XII spectra for the first time. All 18 level energies of the 4d 3 configuration and 39 level energies of the strongly interacting 4d 2 4f and 4p 5 4d 4 configurations were established in the Sn XII spectrum. The energy differences between the majority of the 4d m levels and about 40 levels of the 4d m-1 4f+4p 5 4d m+1 configurations were determined in each of the Sn IX, Sn X and Sn XI spectra (m=6-4). As a result, all intense lines were classified in the 130-140 A region relevant to the extreme ultraviolet (EUV) lithography. It was shown that the most of the intense lines in the 2% bandwidth at 135 A belong to the transitions in the Sn XI-Sn XIII spectra

Petroleum potential of dysaerobic carbonate source rocks in an intra-shelf basin: the Lower Cretaceous of Provence, France

Energy Technology Data Exchange (ETDEWEB)

Machhour, L.; Oudin, J.-L.; Lambert, B.; Lapointe, P. [TOTAL, Centre Scientifique et Technique, Saint-Remy-les-Chevreuse, 78 (France); Masse, J.-P. [Universite de Provence, Centre de Sedimentologie-Paleontologie, Marseille, 13 (France)

1998-05-01

Barremian-Aptian Carbonate sediments in southern Provence belong to a drowning sequence within an intra-shelf basin and display organic-carbon-rich horizons corresponding to the demise of a rudists platform system and the onset of dysaerobic conditions. These horizons depart from the classical anoxic model accepted for most marine organic-carbon-rich deposits. They have a rich and diverse fauna documenting nutrient-rich waters with low oxygen content - an environment in which organic matter is preserved from both biological and chemical degradation. Sedimentological, geochemical and palaeoecological investigations suggest that the organic-carbon-rich carbonates reflect dysaerobic conditions favourable for organic matter preservation, the amount of dissolved oxygen being lower than the geochemical threshold for organic matter decay. These organic-carbon-rich sediments are the result of high sea surface productivity and sea bottom conditions favouring preservation. The kerogen is mainly amorphous sapropelic organic matter, essentially algal, with a high hydrogen index and is of marine origin, deposited during high sea-level. (Author)

Adaptive Processing for Sequence Alignment

KAUST Repository

Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

2012-01-01

Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

Adaptive Processing for Sequence Alignment

KAUST Repository

Zidan, Mohammed A.

2012-01-26

Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

The distribution of organic carbon fractions in a typical loess-paleosol profile and its paleoenvironmental significance

Directory of Open Access Journals (Sweden)

Qingqing Zhang

2018-04-01

Full Text Available Background The loess-paleosol sequence on the Loess Plateau has been considered an important paleoclimatic archive to study global climatic and environmental changes in the Quaternary. So far, little attention has been paid to the characteristics of soil organic carbon fractions in loess-paleosol sequences, which may provide valuable information for exploring the evolution of climate and environment in the Quaternary on the Loess Plateau. Methods In order to explore the significance of mineral-associated organic carbon to total organic carbon (MOC/TOC ratios in the loess-paleosol sequence for reconstructing paleoenvironmental and paleoclimatic evolution in the Quaternary on the Loess Plateau, we selected a typical loess-paleosol profile in Chunhua county, Xianyang city, Shaanxi province, as the research object. The content of total organic carbon (TOC and MOC/TOC ratio in each loess and paleosol layers of the Chunhua loess-paleosol profile were analyzed, together with the paleoclimatic proxies, such as soil grain size, CaCO3 content and their correlations with organic carbon parameters. Results The main results were as follows: (1 the total content of soil organic carbon and MOC/TOC ratios were generally higher in paleosol layers than in the underlying loess layers of the Chunhua loess-paleosol profile. Compared to total organic carbon content, MOC/TOC ratios changed more obviously in soil layers below a paleosol layer S8; (2 soil clay content and median grain size (Md (ϕ were higher in paleosol than in the underlying loess, while CaCO3 content showed an opposite tendency. In the Chunhua profile, the distribution characteristics of the three paleoclimatic proxies showed good indications of paleoclimate changes in the Quaternary; (3 in the Chunhua loess-paleosol profile, MOC/TOC ratios were positively correlated with clay content and median grain size (ϕ, while negatively correlated with CaCO3 content, and the correlations were more significant

The distribution of organic carbon fractions in a typical loess-paleosol profile and its paleoenvironmental significance

Science.gov (United States)

Hu, Feinan; Huo, Na; Shang, Yingni; Chang, Wenqian

2018-01-01

Background The loess-paleosol sequence on the Loess Plateau has been considered an important paleoclimatic archive to study global climatic and environmental changes in the Quaternary. So far, little attention has been paid to the characteristics of soil organic carbon fractions in loess-paleosol sequences, which may provide valuable information for exploring the evolution of climate and environment in the Quaternary on the Loess Plateau. Methods In order to explore the significance of mineral-associated organic carbon to total organic carbon (MOC/TOC) ratios in the loess-paleosol sequence for reconstructing paleoenvironmental and paleoclimatic evolution in the Quaternary on the Loess Plateau, we selected a typical loess-paleosol profile in Chunhua county, Xianyang city, Shaanxi province, as the research object. The content of total organic carbon (TOC) and MOC/TOC ratio in each loess and paleosol layers of the Chunhua loess-paleosol profile were analyzed, together with the paleoclimatic proxies, such as soil grain size, CaCO3 content and their correlations with organic carbon parameters. Results The main results were as follows: (1) the total content of soil organic carbon and MOC/TOC ratios were generally higher in paleosol layers than in the underlying loess layers of the Chunhua loess-paleosol profile. Compared to total organic carbon content, MOC/TOC ratios changed more obviously in soil layers below a paleosol layer S8; (2) soil clay content and median grain size (Md (ϕ)) were higher in paleosol than in the underlying loess, while CaCO3 content showed an opposite tendency. In the Chunhua profile, the distribution characteristics of the three paleoclimatic proxies showed good indications of paleoclimate changes in the Quaternary; (3) in the Chunhua loess-paleosol profile, MOC/TOC ratios were positively correlated with clay content and median grain size (ϕ), while negatively correlated with CaCO3 content, and the correlations were more significant in soil

Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

Directory of Open Access Journals (Sweden)

Marta Brozynska

Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

Microbial diversity and carbon cycling in San Francisco Bay wetlands

Energy Technology Data Exchange (ETDEWEB)

Theroux, Susanna [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Hartman, Wyatt [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; He, Shaomei [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Univ. of Wisconsin, Madison, WI (United States); Tringe, Susannah [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.

2014-03-21

Wetland restoration efforts in San Francisco Bay aim to rebuild habitat for endangered species and provide an effective carbon storage solution, reversing land subsidence caused by a century of industrial and agricultural development. However, the benefits of carbon sequestration may be negated by increased methane production in newly constructed wetlands, making these wetlands net greenhouse gas (GHG) sources to the atmosphere. We investigated the effects of wetland restoration on below-ground microbial communities responsible for GHG cycling in a suite of historic and restored wetlands in SF Bay. Using DNA and RNA sequencing, coupled with real-time GHG monitoring, we profiled the diversity and metabolic potential of wetland soil microbial communities. The wetland soils harbor diverse communities of bacteria and archaea whose membership varies with sampling location, proximity to plant roots and sampling depth. Our results also highlight the dramatic differences in GHG production between historic and restored wetlands and allow us to link microbial community composition and GHG cycling with key environmental variables including salinity, soil carbon and plant species.

REE in the Griqualand-West carbonates - evidence for seawater/fresh water mixing?

International Nuclear Information System (INIS)

Danielson, A.

1990-01-01

The investigated sample material is derived from the carbonate buildup of the Transvaal Supergoup in an area between Schmitsdrift and Griquatown and Danielskuil and Douglas. Out of the stratigraphic sequence samples from seven formations have been analyzed. The studied material represents a wide range of environmental settings, from platform margin up to intertidal conditions. Various stages of dolomitization are present. 1 ref., 1 fig

Carbon, nitrogen, and oxygen abundances in main-sequence stars. II. 20 F and G stars

International Nuclear Information System (INIS)

Clegg, R.E.S.; Lambert, D.L.; Tomkin, J.

1981-01-01

High-resolution Reticon spectra of red and near-infrared C I, N I, and O I lines have been analyzed to determine C, N, and O abundances in a sample of 20 F and G main-sequence stars. Their iron abundances, which have been determined from analysis of additional Reticon spectra of red Fe I lines, cover the range -0.9< or =[Fe/H]< or =+0.4. Sulfur abundances have also been obtained

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

Science.gov (United States)

Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

2017-07-01

PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

Allele Re-sequencing Technologies

DEFF Research Database (Denmark)

Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

2013-01-01

The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

Integral Ring Carbon-Carbon Piston

Science.gov (United States)

Northam, G. Burton (Inventor)

1999-01-01

An improved structure for a reciprocating internal combustion engine or compressor piston fabricate from carbon-carbon composite materials is disclosed. An integral ring carbon-carbon composite piston, disclosed herein, reduces the need for piston rings and for small clearances by providing a small flexible, integral component around the piston that allows for variation in clearance due to manufacturing tolerances, distortion due to pressure and thermal loads, and variations in thermal expansion differences between the piston and cylinder liner.

Distribution of ancient carbon in buried soils in an eroding loess landscape

Science.gov (United States)

Szymanski, L. M.; Mason, J. A.; De Graaff, M. A.; Berhe, A. A.; Marin-Spiotta, E.

2017-12-01

Understanding the processes that contribute to the accumulation and loss of carbon in soils and the implications for land management is vital for mitigating climate change. Buried soils or paleosols that represent former surface horizons can store more organic carbon than mineral horizons at equivalent depths due to burial restricting microbial decomposition. The presence of buried soils defies modeled expectations of exponential declines in carbon concentrations with depth, especially in locations where successive depositional events lead to multiple buried soil layers. Buried soils are found in a diversity of depositional environments across latitudes and without accounting for their presence can lead to underestimates of regional carbon reservoirs. Here we present data on the spatial distribution of carbon in a paleosol loess sequence in Nebraska, focusing on one prominent paleosol, the Brady soil. The Brady soil has been identified throughout the Central Great Plains and began developing at the end of the Pleistocene and was subsequently buried by loess in the early Holocene (Mason et al. 2003). Preliminary analyses of the Brady soil at its deepest, 6-m below the surface, reveal large differences in the composition and degree of decomposition of organic matter from the modern soil. We sampled along burial and erosional transects to characterize spatial variability in the depth of Brady soil from the modern landscape surface and to determine how these differences may alter the amount and composition of organic carbon. A more accurate determination of the spatial extent and heterogeneity of buried soil carbon will improve regional estimates of carbon reservoirs. This assessment of its variability across the landscape will inform future planned work on the vulnerability of ancient carbon to disturbance.

Design of Long Period Pseudo-Random Sequences from the Addition of -Sequences over

Directory of Open Access Journals (Sweden)

Ren Jian

2004-01-01

Full Text Available Pseudo-random sequence with good correlation property and large linear span is widely used in code division multiple access (CDMA communication systems and cryptology for reliable and secure information transmission. In this paper, sequences with long period, large complexity, balance statistics, and low cross-correlation property are constructed from the addition of -sequences with pairwise-prime linear spans (AMPLS. Using -sequences as building blocks, the proposed method proved to be an efficient and flexible approach to construct long period pseudo-random sequences with desirable properties from short period sequences. Applying the proposed method to , a signal set is constructed.

Calcite Phase Conversion Prediction Model for CaO-Al2O3-SiO2 Slag: An Aqueous Carbonation Process at Ambient Pressure

Science.gov (United States)

Zhang, Huining; Dong, Jianhong; Li, Hui; Xiong, Huihui; Xu, Anjun

2018-06-01

To evaluate the effect of the mineralogical phase on carbonation efficiency for CaO-Al2O3-SiO2 slag, a calcite phase conversion prediction model is proposed. This model combines carbon dioxide solubility with carbonation reaction kinetic analysis to improve the prediction capability. The effect of temperature and carbonation time on the carbonation degree is studied in detail. Results show that the reaction rate constant ranges from 0.0135 h-1 to 0.0458 h-1 and that the mineralogical phase contribution sequence for the carbonation degree is C2S, CaO, C3A and CS. The model accurately predicts the effect of temperature and carbonation time on the simulated calcite conversion, and the results agree with the experimental data. The optimal carbonation temperature and reaction time are 333 K and 90 min, respectively. The maximum carbonation efficiency is about 184.3 g/kg slag, and the simulation result of the calcite phase content in carbonated slag is about 20%.

Carbonic anhydrase 2-like in the giant clam, Tridacna squamosa: characterization, localization, response to light, and possible role in the transport of inorganic carbon from the host to its symbionts.

Science.gov (United States)

Ip, Yuen K; Koh, Clarissa Z Y; Hiong, Kum C; Choo, Celine Y L; Boo, Mel V; Wong, Wai P; Neo, Mei L; Chew, Shit F

2017-12-01

The fluted giant clam, Tridacna squamosa , lives in symbiosis with zooxanthellae which reside extracellularly inside a tubular system. Zooxanthellae fix inorganic carbon (C i ) during insolation and donate photosynthate to the host. Carbonic anhydrases catalyze the interconversion of CO 2 and HCO3-, of which carbonic anhydrase 2 (CA2) is the most ubiquitous and involved in many biological processes. This study aimed to clone a CA2 homolog ( CA2-like ) from the fleshy and colorful outer mantle as well as the thin and whitish inner mantle of T. squamosa , to determine its cellular and subcellular localization, and to examine the effects of light exposure on its gene and protein expression levels. The cDNA coding sequence of CA2-like from T. squamosa comprised 789 bp, encoding 263 amino acids with an estimated molecular mass of 29.6 kDa. A phenogramic analysis of the deduced CA2-like sequence denoted an animal origin. CA2-like was not detectable in the shell-facing epithelium of the inner mantle adjacent to the extrapallial fluid. Hence, CA2-like is unlikely to participate directly in light-enhanced calcification. By contrast, the outer mantle, which contains the highest density of tertiary tubules and zooxanthellae, displayed high level of CA2-like expression, and CA2-like was localized to the tubule epithelial cells. More importantly, exposure to light induced significant increases in the protein abundance of CA2-like in the outer mantle. Hence, CA2-like could probably take part in the increased supply of inorganic carbon (C i ) from the host clam to the symbiotic zooxanthellae when the latter conduct photosynthesis to fix C i during light exposure. © 2017 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and the American Physiological Society.

Characterization of carbon dioxide concentrating chemolithotrophic bacterium Serratia sp. ISTD04 for production of biodiesel.

Science.gov (United States)

Kumar, Manish; Morya, Raj; Gnansounou, Edgard; Larroche, Christian; Thakur, Indu Shekhar

2017-11-01

Proteomics and metabolomics analysis has become a powerful tool for characterization of microbial ability for fixation of Carbon dioxide. Bacterial community of palaeoproterozoic metasediments was enriched in the shake flask culture in the presence of NaHCO 3 . One of the isolate showed resistance to NaHCO 3 (100mM) and was identified as Serratia sp. ISTD04 by 16S rRNA sequence analysis. Carbon dioxide fixing ability of the bacterium was established by carbonic anhydrase enzyme assay along with proteomic analysis by LC-MS/MS. In proteomic analysis 96 proteins were identified out of these 6 protein involved in carbon dioxide fixation, 11 in fatty acid metabolism, indicating the carbon dioxide fixing potency of bacterium along with production of biofuel. GC-MS analysis revealed that hydrocarbons and FAMEs produced by bacteria within the range of C 13 -C 24 and C 11 -C 19 respectively. Presence of 59% saturated and 41% unsaturated organic compounds, make it a better fuel composition. Copyright © 2017 Elsevier Ltd. All rights reserved.

Error Analysis of Deep Sequencing of Phage Libraries: Peptides Censored in Sequencing

Directory of Open Access Journals (Sweden)

Wadim L. Matochko

2013-01-01

Full Text Available Next-generation sequencing techniques empower selection of ligands from phage-display libraries because they can detect low abundant clones and quantify changes in the copy numbers of clones without excessive selection rounds. Identification of errors in deep sequencing data is the most critical step in this process because these techniques have error rates >1%. Mechanisms that yield errors in Illumina and other techniques have been proposed, but no reports to date describe error analysis in phage libraries. Our paper focuses on error analysis of 7-mer peptide libraries sequenced by Illumina method. Low theoretical complexity of this phage library, as compared to complexity of long genetic reads and genomes, allowed us to describe this library using convenient linear vector and operator framework. We describe a phage library as N×1 frequency vector n=ni, where ni is the copy number of the ith sequence and N is the theoretical diversity, that is, the total number of all possible sequences. Any manipulation to the library is an operator acting on n. Selection, amplification, or sequencing could be described as a product of a N×N matrix and a stochastic sampling operator (Sa. The latter is a random diagonal matrix that describes sampling of a library. In this paper, we focus on the properties of Sa and use them to define the sequencing operator (Seq. Sequencing without any bias and errors is Seq=Sa IN, where IN is a N×N unity matrix. Any bias in sequencing changes IN to a nonunity matrix. We identified a diagonal censorship matrix (CEN, which describes elimination or statistically significant downsampling, of specific reads during the sequencing process.

Soil carbon and nitrogen sequestration over an age sequence of Pinus patula plantations in Zimbabwean Eastern Highlands

NARCIS (Netherlands)

Mujuru, L.; Gotora, T.; Velthorst, E.J.; Nyamangara, J.; Hoosbeek, M.R.

2014-01-01

Forests play a major role in regulating the rate of increase of global atmospheric carbon dioxide (CO2) concentrations creating a need to investigate the ability of exotic plantations to sequester atmospheric CO2. This study examined pine plantations located in the Eastern Highlands of Zimbabwe

Depositional facies mosaics and their time lines in Lower Ordovician carbonates of central Appalachians

Energy Technology Data Exchange (ETDEWEB)

Nguyen, C.T.; Goldhammer, R.K.; Hardie, L.A.

1985-02-01

A comparative sedimentology and facies stratigraphy study of the Lower Ordovician carbonate of the central Appalachians (Beekmantown Group and equivalents) has been carried out. Our approach used subfacies (rock record of subenvironments) as the basin units of section measurement. The authors differentiated related sets of subfacies into larger facies units (rock record of environments). Facies were then correlated from section to section using fossils and lithostratigraphy to make a 3-dimensional facies mosaic. Within this mosaic, time lines were constructed using onlap-offlap tongues and cyclic sequences. These time lines cut across facies boundaries. Using this approach, the authors have established that the lower 600 m of the Lower Ordovician carbonate sequence is made up of 4 main facies: (1) cyclic laminite facies composed of a package of shoaling-upward shelf lagoon-peritidal cycles, (2) thin-bedded grainstone facies deposited in a shelf lagoon, (3) Renalcis bioherm facies recording a shelf lagoon patch-reef environment, and (4) Epiphyton bioherm facies recording a shelf-edge reef system. The distribution of these facies along time lines across the strike of the central Appalachians is markedly zoned. Epiphyton bioherm facies dominate the eastern margin while cyclic laminite facies dominate the western margin, with thin-bedded grainstone and Renalcis bioherm facies making up the central belt. This zonation of facies is a typical shallow carbonate shelf system with fringing reefs along the eastern, seaward margin and tidal flats along the western, landward margin. Vertical distribution of these facies across strike records 3 major sea level changes during deposition of the lower 600 m of this extensive Lower Ordovician carbonate shelf.

Ionic liquid-functionalized graphene as modifier for electrochemical and electrocatalytic improvement: comparison of different carbon electrodes.

Science.gov (United States)

Du, Meng; Yang, Tao; Ma, Suyan; Zhao, Changzhi; Jiao, Kui

2011-04-01

Electrochemical activities of typically electrochemical targets at three kinds of modified carbon electrodes, i.e. carbon ionic liquid electrode (CILE), graphene/carbon paste electrode (CPE), and ionic liquid-functionalized graphene (IL-graphene)/CPE, were compared in detail. The redox processes of the probes at IL-graphene/CPE were faster than those at CILE and graphene/CPE from cyclic voltammetry. An electrochemical method for the simultaneous determination of guanine and adenine was described with detection limits of 6.5×10(-8) mol L(-1) (guanine) and 3.2×10(-8) mol L(-1) (adenine). Single A→G mutation of sequence-specific DNA could be discriminated by the IL-graphene/CPE. Copyright © 2011 Elsevier B.V. All rights reserved.

Log-balanced combinatorial sequences

Directory of Open Access Journals (Sweden)

Tomislav Došlic

2005-01-01

Full Text Available We consider log-convex sequences that satisfy an additional constraint imposed on their rate of growth. We call such sequences log-balanced. It is shown that all such sequences satisfy a pair of double inequalities. Sufficient conditions for log-balancedness are given for the case when the sequence satisfies a two- (or more- term linear recurrence. It is shown that many combinatorially interesting sequences belong to this class, and, as a consequence, that the above-mentioned double inequalities are valid for all of them.

Mutagenic effects of carbon ion beam irradiations on dry Lotus japonicus seeds

Energy Technology Data Exchange (ETDEWEB)

Luo, Shanwei [Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zhou, Libin, E-mail: libinzhou@impcas.ac.cn [Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000 (China); Li, Wenjian; Du, Yan [Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000 (China); Yu, Lixia; Feng, Hui; Mu, Jinhu [Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Chen, Yuze [College of Life Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, Gansu Province 730070 (China)

2016-09-15

Carbon ion beam irradiation is a powerful method for creating mutants and has been used in crop breeding more and more. To investigate the effects of carbon ion beams on Lotus japonicus, dry seeds were irradiated by 80 MeV/u carbon ion beam at dosages of 0, 100, 200, 300, 400, 500 and 600 Gy. The germination rate, survival rate and root length of M{sub 1} populations were explored and the dose of 400 Gy was selected as the median lethal dose (LD{sub 50}) for a large-scale mutant screening. Among 2472 M{sub 2} plants, 127 morphological mutants including leaf, stem, flower and fruit phenotypic variation were found, and the mutation frequency was approximately 5.14%. Inter simple sequence repeat (ISSR) assays were utilized to investigate the DNA polymorphism between seven mutants and eight plants without phenotypic variation from M{sub 2} populations. No remarkable differences were detected between these two groups, and the total polymorphic rate was 0.567%.

Depositional environments and cyclicity of the Early Ordovician carbonate ramp in the western Tarim Basin (NW China)

Science.gov (United States)

Guo, Chuan; Chen, Daizhao; Song, Yafang; Zhou, Xiqiang; Ding, Yi; Zhang, Gongjing

2018-06-01

During the Early Ordovician, the Tarim Basin (NW China) was mainly occupied by an extensive shallow-water carbonate platform, on which a carbonate ramp system was developed in the Bachu-Keping area of the western part of the basin. Three well-exposed typical outcrop sections of the Lower Ordovician Penglaiba Formation were investigated in order to identify the depositional facies and to clarify origins of meter-scale cycles and depositional sequences, thereby the platform evolution. Thirteen lithofacies are identified and further grouped into three depositional facies (associations): peritidal, restricted and open-marine subtidal facies. These lithofacies are vertically stacked into meter-scale, shallowing-upward peritidal and subtidal cycles. The peritidal cycles are mainly distributed in the lower and uppermost parts of the Penglaiba Formation deposited in the inner-middle ramp, and commonly start with shallow subtidal to intertidal facies followed by inter- to supratidal facies. In contrast, the subtidal cycles occur throughout the formation mostly in the middle-outer ramp and are dominated by shallow to relatively deep (i.e., intermediate) subtidal facies. The dominance of asymmetrical and incomplete cycles suggests a dominant control of Earth's orbital forcing on the cyclic deposition on the platform. On the basis of vertical facies and cycle stacking patterns, and accommodation changes illustrated by the Fischer plots from all studied sections, five third-order depositional sequences are recognized in the Penglaiba Formation. Individual sequences comprise a lower transgressive part and an upper regressive one. In shallow-water depositional environments, the transgressive packages are dominated by thicker-than-average subtidal cycles, indicating an increase in accommodation space, whereas regressive parts are mainly represented by thinner-than-average peritidal and subtidal cycles, denoting a decrease in accommodation space. In contrast, in intermediate to

Chemical Cartography. I. A Carbonicity Map of the Galactic Halo

Energy Technology Data Exchange (ETDEWEB)

Lee, Young Sun; Kim, Young Kwang [Department of Astronomy and Space Science, Chungnam National University, Daejeon 34134 (Korea, Republic of); Beers, Timothy C.; Placco, Vinicius; Yoon, Jinmi [Department of Physics and JINA Center for the Evolution of the Elements, University of Notre Dame, Notre Dame, IN 46556 (United States); Carollo, Daniela [Research School of Astronomy and Astrophysics, The Australian National University, Canberra, ACT 2611 (Australia); Masseron, Thomas [Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HA (United Kingdom); Jung, Jaehun, E-mail: youngsun@cnu.ac.kr [Department of Astronomy, Space Science, and Geology, Chungnam National University, Daejeon 34134 (Korea, Republic of)

2017-02-10

We present the first map of carbonicity, [C/Fe], for the halo system of the Milky Way, based on a sample of over 100,000 main-sequence turnoff stars with available spectroscopy from the Sloan Digital Sky Survey. This map, which explores distances up to 15 kpc from the Sun, reveals clear evidence for the dual nature of the Galactic halo, based on the spatial distribution of stellar carbonicity. The metallicity distribution functions of stars in the inner- and outer-halo regions of the carbonicity map reproduce those previously argued to arise from contributions of the inner- and outer-halo populations, with peaks at [Fe/H] = −1.5 and −2.2, respectively. From consideration of the absolute carbon abundances for our sample, A (C), we also confirm that the carbon-enhanced metal-poor (CEMP) stars in the outer-halo region exhibit a higher frequency of CEMP-no stars (those with no overabundances of heavy neutron-capture elements) than of CEMP- s stars (those with strong overabundances of elements associated with the s -process), whereas the stars in the inner-halo region exhibit a higher frequency of CEMP- s stars. We argue that the contrast in the behavior of the CEMP-no and CEMP- s fractions in these regions arises from differences in the mass distributions of the mini-halos from which the stars of the inner- and outer-halo populations formed, which gives rise in turn to the observed dichotomy of the Galactic halo.

Strength evolution of simulated carbonate-bearing faults: The role of normal stress and slip velocity

Science.gov (United States)

Mercuri, Marco; Scuderi, Marco Maria; Tesei, Telemaco; Carminati, Eugenio; Collettini, Cristiano

2018-04-01

A great number of earthquakes occur within thick carbonate sequences in the shallow crust. At the same time, carbonate fault rocks exhumed from a depth plasticity). We performed friction experiments on water-saturated simulated carbonate-bearing faults for a wide range of normal stresses (from 5 to 120 MPa) and slip velocities (from 0.3 to 100 μm/s). At high normal stresses (σn > 20 MPa) fault gouges undergo strain-weakening, that is more pronounced at slow slip velocities, and causes a significant reduction of frictional strength, from μ = 0.7 to μ = 0.47. Microstructural analysis show that fault gouge weakening is driven by deformation accommodated by cataclasis and pressure-insensitive deformation processes (pressure solution and granular plasticity) that become more efficient at slow slip velocity. The reduction in frictional strength caused by strain weakening behaviour promoted by the activation of pressure-insensitive deformation might play a significant role in carbonate-bearing faults mechanics.

Clinical evaluation of further-developed MRCP sequences in comparison with standard MRCP sequences

International Nuclear Information System (INIS)

Hundt, W.; Scheidler, J.; Reiser, M.; Petsch, R.

2002-01-01

The purpose of this study was the comparison of technically improved single-shot magnetic resonance cholangiopancreatography (MRCP) sequences with standard single-shot rapid acquisition with relaxation enhancement (RARE) and half-Fourier acquired single-shot turbo spin-echo (HASTE) sequences in evaluating the normal and abnormal biliary duct system. The bile duct system of 45 patients was prospectively investigated on a 1.5-T MRI system. The investigation was performed with RARE and HASTE MR cholangiography sequences with standard and high spatial resolutions, and with a delayed-echo half-Fourier RARE (HASTE) sequence. Findings of the improved MRCP sequences were compared with the standard MRCP sequences. The level of confidence in assessing the diagnosis was divided into five groups. The Wilcoxon signed-rank test at a level of p<0.05 was applied. In 15 patients no pathology was found. The MRCP showed stenoses of the bile duct system in 10 patients and choledocholithiasis and cholecystolithiasis in 16 patients. In 12 patients a dilatation of the bile duct system was found. Comparison of the low- and high spatial resolution sequences and the short and long TE times of the half-Fourier RARE (HASTE) sequence revealed no statistically significant differences regarding accuracy of the examination. The diagnostic confidence level in assessing normal or pathological findings for the high-resolution RARE and half-Fourier RARE (HASTE) was significantly better than for the standard sequences. For the delayed-echo half-Fourier RARE (HASTE) sequence no statistically significant difference was seen. The high-resolution RARE and half-Fourier RARE (HASTE) sequences had a higher confidence level, but there was no significant difference in diagnosis in terms of detection and assessment of pathological changes in the biliary duct system compared with standard sequences. (orig.)

Polyadenylated Sequencing Primers Enable Complete Readability of PCR Amplicons Analyzed by Dideoxynucleotide Sequencing

Directory of Open Access Journals (Sweden)

Martin Beránek

2012-01-01

Full Text Available Dideoxynucleotide DNA sequencing is one of the principal procedures in molecular biology. Loss of an initial part of nucleotides behind the 3' end of the sequencing primer limits the readability of sequenced amplicons. We present a method which extends the readability by using sequencing primers modified by polyadenylated tails attached to their 5' ends. Performing a polymerase chain reaction, we amplified eight amplicons of six human genes (AMELX, APOE, HFE, MBL2, SERPINA1 and TGFB1 ranging from 106 bp to 680 bp. Polyadenylation of the sequencing primers minimized the loss of bases in all amplicons. Complete sequences of shorter products (AMELX 106 bp, SERPINA1 121 bp, HFE 208 bp, APOE 244 bp, MBL2 317 bp were obtained. In addition, in the case of TGFB1 products (366 bp, 432 bp, and 680 bp, respectively, the lengths of sequencing readings were significantly longer if adenylated primers were used. Thus, single strand dideoxynucleotide sequencing with adenylated primers enables complete or near complete readability of short PCR amplicons.

Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T.

Directory of Open Access Journals (Sweden)

Ronald M Weiner

2008-05-01

Full Text Available The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40 is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment.

Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Alcanivorax dieselolei KS-293 Isolated from Surface Seawater in the Eastern Mediterranean Sea

KAUST Repository

Barbato, Marta

2015-12-10

We report here the draft genome sequence of Alcanivorax dieselolei KS-293, a hydrocarbonoclastic bacterium isolated from the Mediterranean Sea, by supplying diesel oil as the sole carbon source. This strain contains multiple putative genes associated with hydrocarbon degradation pathways and that are highly similar to those described in A. dieselolei type strain B5.

Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Alcanivorax dieselolei KS-293 Isolated from Surface Seawater in the Eastern Mediterranean Sea

KAUST Repository

Barbato, Marta; Mapelli, Francesca; Chouaia, Bessem; Crotti, Elena; Daffonchio, Daniele; Borin, Sara

2015-01-01

We report here the draft genome sequence of Alcanivorax dieselolei KS-293, a hydrocarbonoclastic bacterium isolated from the Mediterranean Sea, by supplying diesel oil as the sole carbon source. This strain contains multiple putative genes associated with hydrocarbon degradation pathways and that are highly similar to those described in A. dieselolei type strain B5.

Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling

Science.gov (United States)

Chang, Chun-Tien; Tsai, Chi-Neu; Tang, Chuan Yi; Chen, Chun-Houh; Lian, Jang-Hau; Hu, Chi-Yu; Tsai, Chia-Lung; Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Lee, Yun-Shien

2012-01-01

The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. PMID:22778697

Sequence Read Archive (SRA)

Data.gov (United States)

U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

Hierarchical carbon nanostructure design: ultra-long carbon nanofibers decorated with carbon nanotubes

International Nuclear Information System (INIS)

El Mel, A A; Achour, A; Gautron, E; Angleraud, B; Granier, A; Le Brizoual, L; Djouadi, M A; Tessier, P Y; Xu, W; Choi, C H

2011-01-01

Hierarchical carbon nanostructures based on ultra-long carbon nanofibers (CNF) decorated with carbon nanotubes (CNT) have been prepared using plasma processes. The nickel/carbon composite nanofibers, used as a support for the growth of CNT, were deposited on nanopatterned silicon substrate by a hybrid plasma process, combining magnetron sputtering and plasma-enhanced chemical vapor deposition (PECVD). Transmission electron microscopy revealed the presence of spherical nanoparticles randomly dispersed within the carbon nanofibers. The nickel nanoparticles have been used as a catalyst to initiate the growth of CNT by PECVD at 600 deg. C. After the growth of CNT onto the ultra-long CNF, SEM imaging revealed the formation of hierarchical carbon nanostructures which consist of CNF sheathed with CNTs. Furthermore, we demonstrate that reducing the growth temperature of CNT to less than 500 deg. C leads to the formation of carbon nanowalls on the CNF instead of CNT. This simple fabrication method allows an easy preparation of hierarchical carbon nanostructures over a large surface area, as well as a simple manipulation of such material in order to integrate it into nanodevices.

Comparison of impedimetric detection of DNA hybridization on the various biosensors based on modified glassy carbon electrodes with PANHS and nanomaterials of RGO and MWCNTs.

Science.gov (United States)

Benvidi, Ali; Tezerjani, Marzieh Dehghan; Jahanbani, Shahriar; Mazloum Ardakani, Mohammad; Moshtaghioun, Seyed Mohammad

2016-01-15

In this research, we have developed lable free DNA biosensors based on modified glassy carbon electrodes (GCE) with reduced graphene oxide (RGO) and carbon nanotubes (MWCNTs) for detection of DNA sequences. This paper compares the detection of BRCA1 5382insC mutation using independent glassy carbon electrodes (GCE) modified with RGO and MWCNTs. A probe (BRCA1 5382insC mutation detection (ssDNA)) was then immobilized on the modified electrodes for a specific time. The immobilization of the probe and its hybridization with the target DNA (Complementary DNA) were performed under optimum conditions using different electrochemical techniques such as cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The proposed biosensors were used for determination of complementary DNA sequences. The non-modified DNA biosensor (1-pyrenebutyric acid-N- hydroxysuccinimide ester (PANHS)/GCE), revealed a linear relationship between ∆Rct and logarithm of the complementary target DNA concentration ranging from 1.0×10(-16)molL(-1) to 1.0×10(-10)mol L(-1) with a correlation coefficient of 0.992, for DNA biosensors modified with multi-wall carbon nanotubes (MWCNTs) and reduced graphene oxide (RGO) wider linear range and lower detection limit were obtained. For ssDNA/PANHS/MWCNTs/GCE a linear range 1.0×10(-17)mol L(-1)-1.0×10(-10)mol L(-1) with a correlation coefficient of 0.993 and for ssDNA/PANHS/RGO/GCE a linear range from 1.0×10(-18)mol L(-1) to 1.0×10(-10)mol L(-1) with a correlation coefficient of 0.985 were obtained. In addition, the mentioned biosensors were satisfactorily applied for discriminating of complementary sequences from noncomplementary sequences, so the mentioned biosensors can be used for the detection of BRCA1-associated breast cancer. Copyright © 2015. Published by Elsevier B.V.

Implication of using different carbon sources for denitrification in wastewater treatments.

Science.gov (United States)

Cherchi, Carla; Onnis-Hayden, Annalisa; El-Shawabkeh, Ibrahim; Gu, April Z

2009-08-01

Application of external carbon sources for denitrification becomes necessary for wastewater treatment plants that have to meet very stringent effluent nitrogen limits (e.g., 3 to 5 mgTN/L). In this study, we evaluated and compared three carbon sources--MicroC (Environmental Operating Solutions, Bourne, Massachusetts), methanol, and acetate-in terms of their denitrification rates and kinetics, effect on overall nitrogen removal performance, and microbial community structure of carbon-specific denitrifying enrichments. Denitrification rates and kinetics were determined with both acclimated and non-acclimated biomass, obtained from laboratory-scale sequencing batch reactor systems or full-scale plants. The results demonstrate the feasibility of the use of MicroC for denitrification processes, with maximum denitrification rates (k(dmax)) of 6.4 mgN/gVSSh and an observed yield of 0.36 mgVSS/mgCOD. Comparable maximum nitrate uptake rates were found with methanol, while acetate showed a maximum denitrification rate nearly twice as high as the others. The maximum growth rates measured at 20 degrees C for MicroC and methanol were 3.7 and 1.2 day(-1), respectively. The implications resulting from the differences in the denitrification rates and kinetics of different carbon sources on the full-scale nitrogen removal performance, under various configurations and operational conditions, were assessed using Biowin (EnviroSim Associates, Ltd., Flamborough, Ontario, Canada) simulations for both pre- and post-denitrification systems. Examination of microbial population structures using Automated Ribosomal Intergenic Spacer Analysis (ARISA) throughout the study period showed dynamic temporal changes and distinct microbial community structures of different carbon-specific denitrifying cultures. The ability of a specific carbon-acclimated denitrifying population to instantly use other carbon source also was investigated, and the chemical-structure-associated behavior patterns observed

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.

Science.gov (United States)

Huber, Thomas; Faulkner, Geoffrey; Hugenholtz, Philip

2004-09-22

Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments. Bellerophon is available as an interactive web server at http://foo.maths.uq.edu.au/~huber/bellerophon.pl

Carbon Bed Mercury Emissions Control For Mixed Waste Treatment

International Nuclear Information System (INIS)

Soelberg, Nick; Enneking, Joe

2010-01-01

Mercury has had various uses in nuclear fuel reprocessing and other nuclear processes, and so is often present in radioactive and mixed (both radioactive and hazardous according to the Resource Conservation and Recovery Act) wastes. Depending on regulatory requirements, the mercury in the off-gas must be controlled with sometimes very high efficiencies. Compliance to the Hazardous Waste Combustor (HWC) Maximum Achievable Control Technology (MACT) standards can require off-gas mercury removal efficiencies up to 99.999% for thermally treating some mixed waste streams. Several test programs have demonstrated this level of off-gas mercury control using fixed beds of granular sulfur-impregnated activated carbon. Other results of these tests include: (a) The depth of the mercury control mass transfer zone was less than 15-30 cm for the operating conditions of these tests, (b) MERSORB(reg s ign) carbon can sorb Hg up to 19 wt% of the carbon mass, and (c) the spent carbon retained almost all (98-99.99%) of the Hg; but when even a small fraction of the total Hg dissolves, the spent carbon can fail the TCLP test when the spent carbon contains high Hg concentrations. Localized areas in a carbon bed that become heated through heat of adsorption, to temperatures where oxidation occurs, are referred to as 'bed hot spots.' Carbon bed hot spots must be avoided in processes that treat radioactive and mixed waste. Key to carbon bed hot spot mitigation are (a) designing for sufficient gas velocity, for avoiding gas flow maldistribution, and for sufficient but not excessive bed depth, (b) monitoring and control of inlet gas flowrate, temperature, and composition, (c) monitoring and control of in-bed and bed outlet gas temperatures, and (d) most important, monitoring of bed outlet CO concentrations. An increase of CO levels in the off-gas downstream of the carbon bed to levels about 50-100 ppm higher than the inlet CO concentration indicate CO formation in the bed, caused by carbon bed

The Early to Middle Triassic continental–marine transition of NW Bulgaria: sedimentology, palynology and sequence stratigraphy

Directory of Open Access Journals (Sweden)

Ajdanlijsky George

2018-04-01

Full Text Available Sedimentary facies and cycles of the Triassic continental–marine transition of NW Bulgaria are documented in detail from reference sections along the Iskar river gorge between the villages of Tserovo and Opletnya. The depositional environments evolved from anastomosing and meandering river systems in the Petrohan Terrigenous Group to mixed fluvial and tidal settings in the Svidol Formation, and to peritidal and shallow-marine conditions in the Opletnya Member of the Mogila Formation. For the first time, the palynostratigraphic data presented here allow for dating the transitional interval and for the precise identification of a major sequence boundary between the Petrohan Terrigenous Group and the Svidol Formation (Iskar Carbonate Group. This boundary most probably corresponds to the major sequence boundary Ol4 occurring in the upper Olenekian of the Tethyan realm and thus enables interregional correlation. The identification of regionally traceable sequence boundaries based on biostratigraphic age control is a first step towards a more accurate stratigraphic correlation and palaeogeographic interpretation of the Early to early Middle Triassic in NW Bulgaria.

Effect of stacking sequence and surface treatment on the thermal conductivity of multilayered hybrid nano-composites

Science.gov (United States)

Papanicolaou, G. C.; Pappa, E. J.; Portan, D. V.; Kotrotsos, A.; Kollia, E.

2018-02-01

The aim of the present investigation was to study the effect of both the stacking sequence and surface treatment on the thermal conductivity of multilayered hybrid nano-composites. Four types of multilayered hybrid nanocomposites were manufactured and tested: Nitinol- CNTs (carbon nanotubes)- Acrylic resin; Nitinol- Acrylic resin- CNTs; Surface treated Nitinol- CNTs- Acrylic resin and Surface treated Nitinol- Acrylic resin- CNTs. Surface treatment of Nitinol plies was realized by means of the electrochemical anodization. Surface topography of the anodized nitinol sheets was investigated through Scanning Electron Microscopy (SEM). It was found that the overall thermal response of the manufactured multilayered nano-composites was greatly influenced by both the anodization and the stacking sequence. A theoretical model for the prediction of the overall thermal conductivity has been developed considering the nature of the different layers, their stacking sequence as well as the interfacial thermal resistance. Thermal conductivity and Differential Scanning Calorimetry (DSC) measurements were conducted, to verify the predicted by the model overall thermal conductivities. In all cases, a good agreement between theoretical predictions and experimental results was found.

The Early to Middle Triassic continental-marine transition of NW Bulgaria: sedimentology, palynology and sequence stratigraphy

Science.gov (United States)

Ajdanlijsky, George; Götz, Annette E.; Strasser, André

2018-04-01

Sedimentary facies and cycles of the Triassic continental-marine transition of NW Bulgaria are documented in detail from reference sections along the Iskar river gorge between the villages of Tserovo and Opletnya. The depositional environments evolved from anastomosing and meandering river systems in the Petrohan Terrigenous Group to mixed fluvial and tidal settings in the Svidol Formation, and to peritidal and shallow-marine conditions in the Opletnya Member of the Mogila Formation. For the first time, the palynostratigraphic data presented here allow for dating the transitional interval and for the precise identification of a major sequence boundary between the Petrohan Terrigenous Group and the Svidol Formation (Iskar Carbonate Group). This boundary most probably corresponds to the major sequence boundary Ol4 occurring in the upper Olenekian of the Tethyan realm and thus enables interregional correlation. The identification of regionally traceable sequence boundaries based on biostratigraphic age control is a first step towards a more accurate stratigraphic correlation and palaeogeographic interpretation of the Early to early Middle Triassic in NW Bulgaria.

Molecular and elemental analyses of the carbonaceous matter in the gold and uranium bearing Vaal Reef carbon seams, Witwatersrand sequence

International Nuclear Information System (INIS)

Zumberge, J.E.; Sigleo, A.C.; Nagy, B.

1978-01-01

The thin Vaal Reef carbon seams consist of a complex, solid, and solvent insoluble, polymer-like substance, containing mainly hydrocarbons and some organic sulphur and oxygen compounds. These carbon seams are not pure carbon, e.g. graphite, and do not contain only hydrocarbons. According to modern terminology the Vaal Reef carbonaceous matter is most appropriately referred to as kerogen rather than carbon or thucholite. This kerogen is not the result of the polymerization of gaseous or liquid hydrocarbons, but rather of the polymerization of biochemicals from decayed, primitive Precambrian micro-organisms. These microbiota formed mats in which uranium minerals and gold became incorporated before burial under younger sediments. Organic geochemistry was first developed as a means to elucidate the nature and composition of petroleum and coal. Later it was successfully used in lunar sample, planetary surface, and meteorite studies as well as in investigations of kerogens in terrestrial sediments of various ages. Considering economic geology, organic geochemistry holds promise for elucidating the origin and helping in the exploration of carbonaceous ore deposits. The purpose of this report is to review some of the major current organic geochemical methods and to illustrate these by the analysis of the Vaal Reef kerogen. The samples were analysed by a directly connected high vacuum pyrolysis system-gas chromatograph-organic mass spectrometer. Additional analyses were performed by a combined scanning electron microscope-electron microprobe, by the techniques of electron paramagnetic resonance spectroscopy, and by neutron activation analysis

Sol-gel coatings on carbon/carbon composites

International Nuclear Information System (INIS)

Sim, S.M.; Krabill, R.M.; Dalzell, W.J. Jr.; Chu, P.Y.; Clark, D.E.

1986-01-01

The need for structural materials that can withstand severe environments up to 4000 0 F has promulgated the investigation of sol-gel derived ceramic and composite coatings on carbon/carbon composite materials. Alumina and zirconia sols have been deposited via thermophoresis on carbon/carbon substrates

Nickel foam/polyaniline-based carbon/palladium composite electrodes for hydrogen storage

International Nuclear Information System (INIS)

Skowronski, Jan M.; Urbaniak, Jan

2008-01-01

The sandwich-like nickel/palladium/carbon electrodes exhibiting ability to absorb hydrogen in alkaline solution are presented. Electrodes were prepared by successive deposition of palladium and polyaniline layers on nickel foam substrate followed by heat treatment to give Ni/Pd/C electrode. It was shown that thermal conversion of polymer into carbon layer and subsequent thermal activation of carbon component bring about the modification of the mechanism of reversible hydrogen sorption. It was proven that carbon layer, interacting with Pd catalyst, plays a considerable role in the process of hydrogen storage. In the other series of experiments, Pd particles were dispersed electrochemically on carbon coating leading to Ni/C/Pd system. The adding of the next carbon layer resulted in Ni/C/Pd/C electrodes. Electrochemical properties of the electrodes depend on both the sequence of Pd and C layers and the preparation/activation of carbon coating. Electrochemical behavior of sandwich-like electrodes in the reaction of hydrogen sorption/desorption was characterized in 6 M KOH using the cyclic voltammetry method and the results obtained were compared to those for Ni/Pd electrode. The anodic desorption of hydrogen from electrodes free and containing carbon layer was considered after the potentiodynamic as well as potentiostatic sorption of hydrogen. The influence of the sorption potential and the time of rest of electrodes at a cut-off circuit on the kinetics of hydrogen recovery were examined. The results obtained for Ni/Pd/C electrodes indicate that the displacement of hydrogen between C and Pd phase takes place during the rest at a cut-off circuit. Electrodes containing carbon layer require longer time for hydrogen electrosorption. On the other hand, the presence of carbon layer in electrodes is advantageous because a considerable longer retention of hydrogen is possible, as compared to Pd/Ni electrode. Hydrogen stored in sandwich-like electrodes can instantly be

Carbon K-edge spectra of carbonate minerals.

Science.gov (United States)

Brandes, Jay A; Wirick, Sue; Jacobsen, Chris

2010-09-01

Carbon K-edge X-ray spectroscopy has been applied to the study of a wide range of organic samples, from polymers and coals to interstellar dust particles. Identification of carbonaceous materials within these samples is accomplished by the pattern of resonances in the 280-320 eV energy region. Carbonate minerals are often encountered in the study of natural samples, and have been identified by a distinctive resonance at 290.3 eV. Here C K-edge and Ca L-edge spectra from a range of carbonate minerals are presented. Although all carbonates exhibit a sharp 290 eV resonance, both the precise position of this resonance and the positions of other resonances vary among minerals. The relative strengths of the different carbonate resonances also vary with crystal orientation to the linearly polarized X-ray beam. Intriguingly, several carbonate minerals also exhibit a strong 288.6 eV resonance, consistent with the position of a carbonyl resonance rather than carbonate. Calcite and aragonite, although indistinguishable spectrally at the C K-edge, exhibited significantly different spectra at the Ca L-edge. The distinctive spectral fingerprints of carbonates provide an identification tool, allowing for the examination of such processes as carbon sequestration in minerals, Mn substitution in marine calcium carbonates (dolomitization) and serpentinization of basalts.

Carbon K-edge Spectra of Carbonate Minerals

Energy Technology Data Exchange (ETDEWEB)

Brandes, J.; Wirick, S; Jacobsen, C

2010-01-01

Carbon K-edge X-ray spectroscopy has been applied to the study of a wide range of organic samples, from polymers and coals to interstellar dust particles. Identification of carbonaceous materials within these samples is accomplished by the pattern of resonances in the 280-320 eV energy region. Carbonate minerals are often encountered in the study of natural samples, and have been identified by a distinctive resonance at 290.3 eV. Here C K-edge and Ca L-edge spectra from a range of carbonate minerals are presented. Although all carbonates exhibit a sharp 290 eV resonance, both the precise position of this resonance and the positions of other resonances vary among minerals. The relative strengths of the different carbonate resonances also vary with crystal orientation to the linearly polarized X-ray beam. Intriguingly, several carbonate minerals also exhibit a strong 288.6 eV resonance, consistent with the position of a carbonyl resonance rather than carbonate. Calcite and aragonite, although indistinguishable spectrally at the C K-edge, exhibited significantly different spectra at the Ca L-edge. The distinctive spectral fingerprints of carbonates provide an identification tool, allowing for the examination of such processes as carbon sequestration in minerals, Mn substitution in marine calcium carbonates (dolomitization) and serpentinization of basalts.

Hyperspherical functions and quantum-mechanical three-body problem with application to carbon 12

International Nuclear Information System (INIS)

Letz, H.

1975-01-01

In this work a system of three identical particles (bosons) interacting by a particular two-body force is discussed. Using the complete set of the hyperspherical functions (K-harmonics), analytical expressions for eigenvalues and wave functions of the stationary states are found. The numerical evaluation gives a level sequence for a definite pair of potential parameters similar to that of the nucleus carbon 12

Preparation and characterization of carbon/SiC nanowire/Na-doped carbonated hydroxyapatite multilayer coating for carbon/carbon composites

International Nuclear Information System (INIS)

Leilei, Zhang; Hejun, Li; Kezhi, Li; Shouyang, Zhang; Qiangang, Fu; Yulei, Zhang; Jinhua, Lu; Wei, Li

2014-01-01

Highlights: • CSH coatings were prepared by combination of magnetron sputter ion plating, CVD and UECD. • Na + and CO 3 2− were developed to co-substitute hydroxyapatite. • SiC nanowires were introduced into Na-doped carbonated hydroxyapatite. • CSH coatings showed excellent cell activity and cell proliferation behavior. - Abstract: A carbon/SiC nanowire/Na-doped carbonated hydroxyapatite multilayer coating (CSH coating) was prepared on carbon/carbon composites using a combination method of magnetron sputter ion plating, chemical vapor deposition and ultrasound-assisted electrochemical deposition procedure. The morphology, microstructure and chemical composition of the coating were investigated by scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy and X-ray photoelectron spectroscopy (XPS). The results showed that the CSH coating was consisted of three components: carbon layer, SiC nanowires and Na-doped carbonated hydroxyapatite. The carbon layer provided a dense and uniform surface structure for the growth of SiC nanowires. The SiC nanowires exhibited a porous structure, favoring the infiltration of Na-doped carbonated hydroxyapatite crystals. The Na-doped carbonated hydroxyapatite could infiltrate into the pores of SiC nanowires and finally cover the SiC nanowires entirely with a needle shape. The osteoblast-like MG63 cells were employed to assess the in vitro biocompatibility of the CSH coating. The MG63 cells favorably spread and grew well across the CSH coating surface with plenty of filopods and microvilli, exhibiting excellent cell activity. Moreover, the CSH coating elicited higher cell proliferation as compared to bare carbon/carbon composites. In conclusion, the CSH offers great potential as a coating material for future medical application in hard tissue replacement

Preparation and characterization of carbon/SiC nanowire/Na-doped carbonated hydroxyapatite multilayer coating for carbon/carbon composites

Energy Technology Data Exchange (ETDEWEB)

Leilei, Zhang, E-mail: zhangleilei1121@aliyun.com; Hejun, Li; Kezhi, Li; Shouyang, Zhang; Qiangang, Fu; Yulei, Zhang; Jinhua, Lu; Wei, Li

2014-09-15

Highlights: • CSH coatings were prepared by combination of magnetron sputter ion plating, CVD and UECD. • Na{sup +} and CO{sub 3}{sup 2−} were developed to co-substitute hydroxyapatite. • SiC nanowires were introduced into Na-doped carbonated hydroxyapatite. • CSH coatings showed excellent cell activity and cell proliferation behavior. - Abstract: A carbon/SiC nanowire/Na-doped carbonated hydroxyapatite multilayer coating (CSH coating) was prepared on carbon/carbon composites using a combination method of magnetron sputter ion plating, chemical vapor deposition and ultrasound-assisted electrochemical deposition procedure. The morphology, microstructure and chemical composition of the coating were investigated by scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy and X-ray photoelectron spectroscopy (XPS). The results showed that the CSH coating was consisted of three components: carbon layer, SiC nanowires and Na-doped carbonated hydroxyapatite. The carbon layer provided a dense and uniform surface structure for the growth of SiC nanowires. The SiC nanowires exhibited a porous structure, favoring the infiltration of Na-doped carbonated hydroxyapatite crystals. The Na-doped carbonated hydroxyapatite could infiltrate into the pores of SiC nanowires and finally cover the SiC nanowires entirely with a needle shape. The osteoblast-like MG63 cells were employed to assess the in vitro biocompatibility of the CSH coating. The MG63 cells favorably spread and grew well across the CSH coating surface with plenty of filopods and microvilli, exhibiting excellent cell activity. Moreover, the CSH coating elicited higher cell proliferation as compared to bare carbon/carbon composites. In conclusion, the CSH offers great potential as a coating material for future medical application in hard tissue replacement.

Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

DEFF Research Database (Denmark)

de Souza, S J; Camargo, A A; Briones, M R

2000-01-01

Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central ...

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

Science.gov (United States)

Martin, Andrew C R

2014-01-01

The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.

Forming mechanism of the Ordovician karst carbonate reservoirs on the northern slope of central Tarim Basin

Directory of Open Access Journals (Sweden)

Heng Fu

2017-07-01

Full Text Available The Ordovician karst carbonate reservoirs on the northern slope of central Tarim Basin are important oil and gas exploration targets in the basin, but their dissolution mechanisms are in controversy. In this paper, based on the integrated study of sedimentation, sequence and reservoir, together with microscopic analysis and macroscopic seismic data analysis, the carbonate karst reservoirs in the study area were divided into three types: dissolved pore-cavity limestone reservoir, pore-cavity dolomite reservoir and fracture-cavity siliceous reservoir, and their forming mechanisms were discussed respectively. Some findings were obtained. First, dissolved pore-cavity limestone reservoirs are distributed in the upper Yingshan Fm and Yijianfang Fm of the Ordovician vertically, while pore-cavity dolomite reservoirs are mainly developed in the Penglai Fm and lower Yingshan Fm of the Ordovician with great thickness. Second, dissolved pore-cavity limestone reservoirs were formed by karstification on the third-order sequence boundary (lowstand tract, while pore-cavity dolomite reservoirs were formed by deep burial dolomitization controlled by karstification on the third-order sequence boundary, both of which are distributed in the highstand tract below the third-order sequence boundary. Third, siliceous reservoirs are developed under the control of faulting, as a result of reworking of deep hydrothermal fluids along faults to the limestone, and the siliceous reservoirs and their hydrothermal solution fracture-cavity systems are distributed near faults. It is further predicted that, in addition to the three types of reservoir above, platform-margin reef-flat reservoirs are developed in the Ordovician on the northern slope of central Tarim Basin.

Automated cleaning and pre-processing of immunoglobulin gene sequences from high-throughput sequencing

Directory of Open Access Journals (Sweden)

Miri eMichaeli

2012-12-01

Full Text Available High throughput sequencing (HTS yields tens of thousands to millions of sequences that require a large amount of pre-processing work to clean various artifacts. Such cleaning cannot be performed manually. Existing programs are not suitable for immunoglobulin (Ig genes, which are variable and often highly mutated. This paper describes Ig-HTS-Cleaner (Ig High Throughput Sequencing Cleaner, a program containing a simple cleaning procedure that successfully deals with pre-processing of Ig sequences derived from HTS, and Ig-Indel-Identifier (Ig Insertion – Deletion Identifier, a program for identifying legitimate and artifact insertions and/or deletions (indels. Our programs were designed for analyzing Ig gene sequences obtained by 454 sequencing, but they are applicable to all types of sequences and sequencing platforms. Ig-HTS-Cleaner and Ig-Indel-Identifier have been implemented in Java and saved as executable JAR files, supported on Linux and MS Windows. No special requirements are needed in order to run the programs, except for correctly constructing the input files as explained in the text. The programs' performance has been tested and validated on real and simulated data sets.

Carbon and carbon-14 in lunar soil 14163

International Nuclear Information System (INIS)

Fireman, E.L.; Stoenner, R.W.

1981-01-01

Carbon is removed from the surface of lunar soil 14163 size fractions by combustions at 500 and 1000 0 C in an oxygen stream and the carbon contents and the carbon-14 activities are measured. The carbon contents are inversely correlated with grain size. A measured carbon content of 198 ppM for bulk 14163, obtained by combining the size fraction results, is modified to 109 +- 12 ppM by a carbon contamination correction. This value is in accord with a previous determination, 110 ppM, for bulk 14163. The small ( 53 μ) grains, 11.2 +- 2.0 dpm/kg. The combusted carbon and carbon-14 are attributed mainly to solar-wind implantation. Melt extractions of carbon-14 from the combusted soil samples gave essentially identical activities, 21.0 +- 1.5 and 19.2 +- 2.0 dpm/kg for the small and large grains, and are attributed to cosmic-ray spallation-produced carbon-14

Improving the corrosion resistance of proton exchange membrane fuel cell carbon supports by pentafluorophenyl surface functionalization

Science.gov (United States)

Forouzandeh, Farisa; Li, Xiaoan; Banham, Dustin W.; Feng, Fangxia; Joseph Kakanat, Abraham; Ye, Siyu; Birss, Viola

2018-02-01

In this study, the effect of surface functionalization on the electrochemical corrosion resistance of a high surface area, mesoporous colloid imprinted carbon powder (CIC), as well as microporous Vulcan carbon (VC, serving as the benchmark), was demonstrated, primarily for PEM fuel cell applications. CIC-22, which is highly hydrophilic and was synthesized with 22 nm silica colloid templates, and as-received, mildly hydrophobic, VC powders, were functionalized with 2,3,4,5,6-pentafluorophenyl (-PhF5) surface groups using a straightforward diazonium reduction reaction. These carbons were then subjected to corrosion testing, involving a potential cycling-step sequence in room temperature 0.5 M H2SO4. Using cyclic voltammetry and charge/time analysis, the double layer and pseudo-capacitive gravimetric charges of the carbons, prior to and after the application of these potential steps, were tracked in order to obtain information about surface area changes and the extent of carbon oxidation, respectively. It is shown that the corrosion resistance was improved by ca. 50-80% by surface functionalization, likely due to a combination of surface passivation (loss of carbon active sites) and increased surface hydrophobicity.

DNA nanosensor based on biocompatible graphene quantum dots and carbon nanotubes.

Science.gov (United States)

Qian, Zhao Sheng; Shan, Xiao Yue; Chai, Lu Jing; Ma, Juan Juan; Chen, Jian Rong; Feng, Hui

2014-10-15

An ultrasensitive nanosensor based on fluorescence resonance energy transfer (FRET) between biocompatible graphene quantum dots and carbon nanotubes for DNA detection was reported. We take advantage of good biocompatibility and strong fluorescence of graphene quantum dots, base pairing specificity of DNA and unique fluorescence resonance energy transfer between graphene quantum dots and carbon nanotubes to achieve the analysis of low concentrations of DNA. Graphene quantum dots with high quantum yield up to 0.20 were prepared and served as the fluorophore of DNA probe. FRET process between graphene quantum dots-labeled probe and oxidized carbon nanotubes is easily achieved due to their efficient self-assembly through specific π-π interaction. This nanosensor can distinguish complementary and mismatched nucleic acid sequences with high sensitivity and good reproducibility. The detection method based on this nanosensor possesses a broad linear span of up to 133.0 nM and ultralow detection limit of 0.4 nM. The constructed nanosensor is expected to be highly biocompatible because of all its components with excellent biocompatibility. Copyright © 2014 Elsevier B.V. All rights reserved.

Carbon black vs. black carbon and other airborne materials containing elemental carbon: Physical and chemical distinctions

International Nuclear Information System (INIS)

Long, Christopher M.; Nascarella, Marc A.; Valberg, Peter A.

2013-01-01

Airborne particles containing elemental carbon (EC) are currently at the forefront of scientific and regulatory scrutiny, including black carbon, carbon black, and engineered carbon-based nanomaterials, e.g., carbon nanotubes, fullerenes, and graphene. Scientists and regulators sometimes group these EC-containing particles together, for example, interchangeably using the terms carbon black and black carbon despite one being a manufactured product with well-controlled properties and the other being an undesired, incomplete-combustion byproduct with diverse properties. In this critical review, we synthesize information on the contrasting properties of EC-containing particles in order to highlight significant differences that can affect hazard potential. We demonstrate why carbon black should not be considered a model particle representative of either combustion soots or engineered carbon-based nanomaterials. Overall, scientific studies need to distinguish these highly different EC-containing particles with care and precision so as to forestall unwarranted extrapolation of properties, hazard potential, and study conclusions from one material to another. -- Highlights: •Major classes of elemental carbon-containing particles have distinct properties. •Despite similar names, carbon black should not be confused with black carbon. •Carbon black is distinguished by a high EC content and well-controlled properties. •Black carbon particles are characterized by their heterogenous properties. •Carbon black is not a model particle representative of engineered nanomaterials. -- This review demonstrates the significant physical and chemical distinctions between elemental carbon-containing particles e.g., carbon black, black carbon, and engineered nanomaterials

Multilocus Sequence Analysis and rpoB Sequencing of Mycobacterium abscessus (Sensu Lato) Strains▿

Science.gov (United States)

Macheras, Edouard; Roux, Anne-Laure; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby; Bodmer, Thomas; Cambau, Emmanuelle; Gaillard, Jean-Louis; Heym, Beate

2011-01-01

Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536T, M. massiliense CIP 108297T, and M. bolletii CIP 108541T) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the clustering

Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains.

Science.gov (United States)

Macheras, Edouard; Roux, Anne-Laure; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby; Bodmer, Thomas; Cambau, Emmanuelle; Gaillard, Jean-Louis; Heym, Beate

2011-02-01

Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536(T), M. massiliense CIP 108297(T), and M. bolletii CIP 108541(T)) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the

Solid phase extraction of uranium(VI) onto benzoylthiourea-anchored activated carbon

International Nuclear Information System (INIS)

Zhao Yongsheng; Liu Chunxia; Feng Miao; Chen Zhen; Li Shuqiong; Tian Gan; Wang Li; Huang Jingbo; Li Shoujian

2010-01-01

A new solid phase extractant selective for uranium(VI) based on benzoylthiourea anchored to activated carbon was developed via hydroxylation, amidation and reaction with benzoyl isothiocyanate in sequence. Fourier transform infrared spectroscopy and total element analysis proved that benzoylthiourea had been successfully grafted to the surface of the activated carbon, with a loading capacity of 1.2 mmol benzoylthiourea per gram of activated carbon. The parameters that affect the uranium(VI) sorption, such as contact time, solution pH, initial uranium(VI) concentration, adsorbent dose and temperature, have been investigated. Results have been analyzed by Langmuir and Freundlich isotherm; the former was more suitable to describe the sorption process. The maximum sorption capacity (82 mg/g) for uranium(VI) was obtained at experimental conditions. The rate constant for the uranium sorption by the as-synthesized extractant was 0.441 min -1 from the first order rate equation. Thermodynamic parameters (ΔH 0 = -46.2 kJ/mol; ΔS 0 = -98.0 J/mol K; ΔG 0 = -17.5 kJ/mol) showed the adsorption of an exothermic process and spontaneous nature, respectively. Additional studies indicated that the benzoylthiourea-anchored activated carbon (BT-AC) selectively sorbed uranyl ions in the presence of competing ions, Na + , Co 2+ , Sr 2+ , Cs + and La 3+ .

Ingestion of a carbonated beverage decreases lower esophageal sphincter pressure and increases frequency of transient lower esophageal sphincter relaxation in normal subjects.

Science.gov (United States)

Shukla, Akash; Meshram, Megha; Gopan, Amrit; Ganjewar, Vaibhav; Kumar, Praveen; Bhatia, Shobna J

2012-06-01

Transient lower esophageal sphincter relaxation (tLESR) and decreased basal lower esophageal sphincter (LES) pressure are postulated mechanisms of gastroesophageal reflux (GER). There is conflicting evidence on the effect of carbonated drinks on lower esophageal sphincter function. This study was conducted to assess the effect of a carbonated beverage on tLESR and LES pressure. High resolution manometry tracings (16 channel water-perfused, Trace 1.2, Hebbard, Australia) were obtained in 18 healthy volunteers (6 men) for 30 min each at baseline, and after 200 mL of chilled potable water and 200 mL of chilled carbonated cola drink (Pepsi [Pepsico India Ltd]). The sequence of administration of the drinks was determined by random number method generated by a computer. The analysis of tracings was done using TRACE 1.2 software by a physician who was unaware of the sequence of administration of fluids. The mean (SD) age of the participant was 37.3 (12.9) years. The median (range) frequency of tLESr was higher after the carbonated beverage (10.5 [0-26]) as compared to baseline (0 [0-3], p = 0.005) as well as after water (1 [0-14], p = 0.010). The LES pressure decreased after ingestion of the carbonated beverage (18.5 [11-37] mmHg) compared to baseline (40.5 [25-66] mmHg, p = 0.0001) and after water (34 [15-67] mmHg, p = 0.003). Gastric pressure was not different in the three groups. Ingestion of a carbonated beverage increases tLESr and lowers LES pressure in healthy subjects.

The efficiency of seismic attributes to differentiate between massive and non-massive carbonate successions for hydrocarbon exploration activity

Science.gov (United States)

Sarhan, Mohammad Abdelfattah

2017-12-01

The present work investigates the efficiency of applying volume seismic attributes to differentiate between massive and non-massive carbonate sedimentary successions on using seismic data. The main objective of this work is to provide a pre-drilling technique to recognize the porous carbonate section (probable hydrocarbon reservoirs) based on seismic data. A case study from the Upper Cretaceous - Eocene carbonate successions of Abu Gharadig Basin, northern Western Desert of Egypt has been tested in this work. The qualitative interpretations of the well-log data of four available wells distributed in the study area, namely; AG-2, AG-5, AG-6 and AG-15 wells, has confirmed that the Upper Cretaceous Khoman A Member represents the massive carbonate section whereas the Eocene Apollonia Formation represents the non-massive carbonate unit. The present work have proved that the most promising seismic attributes capable of differentiating between massive and non-massive carbonate sequences are; Root Mean Square (RMS) Amplitude, Envelope (Reflection Strength), Instantaneous Frequency, Chaos, Local Flatness and Relative Acoustic Impedance.

ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS

Directory of Open Access Journals (Sweden)

Alves-Ferreira Marcelo

2008-09-01

Full Text Available Abstract Background Genome survey sequences (GSS offer a preliminary global view of a genome since, unlike ESTs, they cover coding as well as non-coding DNA and include repetitive regions of the genome. A more precise estimation of the nature, quantity and variability of repetitive sequences very early in a genome sequencing project is of considerable importance, as such data strongly influence the estimation of genome coverage, library quality and progress in scaffold construction. Also, the elimination of repetitive sequences from the initial assembly process is important to avoid errors and unnecessary complexity. Repetitive sequences are also of interest in a variety of other studies, for instance as molecular markers. Results We designed and implemented a straightforward pipeline called ReRep, which combines bioinformatics tools for identifying repetitive structures in a GSS dataset. In a case study, we first applied the pipeline to a set of 970 GSSs, sequenced in our laboratory from the human pathogen Leishmania braziliensis, the causative agent of leishmaniosis, an important public health problem in Brazil. We also verified the applicability of ReRep to new sequencing technologies using a set of 454-reads of an Escheria coli. The behaviour of several parameters in the algorithm is evaluated and suggestions are made for tuning of the analysis. Conclusion The ReRep approach for identification of repetitive elements in GSS datasets proved to be straightforward and efficient. Several potential repetitive sequences were found in a L. braziliensis GSS dataset generated in our laboratory, and further validated by the analysis of a more complete genomic dataset from the EMBL and Sanger Centre databases. ReRep also identified most of the E. coli K12 repeats prior to assembly in an example dataset obtained by automated sequencing using 454 technology. The parameters controlling the algorithm behaved consistently and may be tuned to the properties

sequenceMiner algorithm

Data.gov (United States)

National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

Carbon/carbon composite materials

International Nuclear Information System (INIS)

Thebault, J.; Orly, P.

2006-01-01

Carbon/carbon composites are singular materials from their components, their manufacturing process as well as their characteristics. This paper gives a global overview of these particularities and applications which make them now daily used composites. (authors)

11 things a geologist thinks an engineer should know about carbonate beaches

Science.gov (United States)

Halley, Robert B.; Magoon, Orville T.; Robbins, Lisa L.; Ewing, Lesley

2002-01-01

This is a review of the geological aspects of carbonate beaches that a geologist thinks may be useful for an engineer. Classical geologic problems of carbonate beaches, for example how ancient examples are recognized in rock sequences, are of little interest to engineers. Geologists not involved in engineering problems may find it difficult to know what an engineer should understand about carbonate beaches. Nevertheless, there are at least eleven topics that are potentially very useful for engineers to keep in mind. These eleven are chosen with as much thought going into what has been omitted as has been given to the eleven included topics. Some qualifications are in order: First, this paper does not discuss certain kinds of carbonate shorelines that are beyond the scope of engineering issues. For example, this review does not discuss very high-energy carbonate boulder beaches. These beaches are comprised of pieces of carbonate material ganging in size from ten centimeters to meters. Typically, these are high-energy storm deposits formed from pieces of either eroded carbonate rock or other large carbonate pieces such as pieces of large corals. This paper focuses on sand-sized (0.0625–2.0 mm) coastal carbonate deposits. Second, offshore beaches will not be discussed. There are many carbonate beaches that form on banks or shoals exposed at low tide, but our discussion is confined to what most people think of when they go to some tropical island and/or resort and walk out to lay on the beach. Third, this paper does not consider mixed carbonate/quartz sand beaches. While mixed beaches are common, only the end member of purely carbonate sand beaches is considered. Fourth, there will be no order of preference of the eleven topics. And lastly, these eleven topics are not consensus items. These are simply one geologist s thoughts about the aspects of carbonate beaches that would be useful for engineering colleagues to keep in mind. Where possible, general reference is

Synthesis of carbon nanorods by reduction of carbon bisulfide

International Nuclear Information System (INIS)

Lou Zhengsong; He Minglong; Zhao Dejian; Li Zhongchun; Shang Tongming

2010-01-01

Research highlights: Our manuscript is a concise preliminary account of original and of significant research, which illuminates carbon nanorods and variously shaped Y-junction carbon nanorods are successfully fabricated on a large scale through a carbon bisulfide thermal reduction process. Various shaped Y-junction carbon nanorods can be used as studying the electronic and transport properties of the nano-meter carbon material. - Abstract: Carbon nanorods are synthesized at large scale by the reduction of carbon bisulfide at 600 o C. Moreover, novel Y-junction carbon nanorods are detected in the samples. The X-ray power diffraction pattern indicates that the products are hexagonal graphite. Scanning electron microscopy, transmission electron microscopy, high-resolution transmission electron microscopy and N 2 physisorption studies show that carbon nanorods predominate in the product. Based on the supercritical carbon bisulfide system, the possible growth mechanism of the carbon nanorods was discussed. This method provides a simple and cheap route to large-scale synthesis of carbon nanorods.

Facile template-directed synthesis of carbon-coated SnO2 nanotubes with enhanced Li-storage capabilities

International Nuclear Information System (INIS)

Zhu, Xiaoshu; Zhu, Jingyi; Yao, Yinan; Zhou, Yiming; Tang, Yawen; Wu, Ping

2015-01-01

Herein, a novel type of carbon-coated SnO 2 nanotubes has been designed and synthesized through a facile two-step hydrothermal approach by using ZnO nanorods as templates. During the synthetic route, SnO 2 nanocrystals and carbon layer have been uniformly deposited on the rod-like templates in sequence, meanwhile ZnO nanorods could be in situ dissolved owing to the generated alkaline and acidic environments during hydrothermal coating of SnO 2 nanocrystals and hydrothermal carbonization of glucose, respectively. When utilized as an anode material in lithium-ion batteries, the carbon-coated SnO 2 nanotubes manifests markedly enhanced Li-storage capabilities in terms of specific capacity and cycling stability in comparison with bare SnO 2 nanocrystals. - Graphical abstract: Display Omitted - Highlights: • C-coated SnO 2 nanotubes prepared via facile ZnO-nanorod-templated hydrothermal route. • Unique morphological and structural features toward lithium storage. • Enhanced Li-storage performance in terms of specific capacity and cycling stability

Carbon dioxide sequestration by mineral carbonation

NARCIS (Netherlands)

Huijgen, W.J.J.

2007-01-01

The increasing atmospheric carbon dioxide (CO2) concentration, mainly caused by fossil fuel combustion, has lead to concerns about global warming. A possible technology that can contribute to the reduction of carbon dioxide emissions is CO2 sequestration by mineral carbonation. The basic concept

Water self-diffusion through narrow oxygenated carbon nanotubes

Energy Technology Data Exchange (ETDEWEB)

Striolo, Alberto [School of Chemical Biological and Materials Engineering, University of Oklahoma, Norman, OK 73019 (United States)

2007-11-28

The hydrophobic interior of carbon nanotubes, which is reminiscent of ion channels in cellular membranes, has inspired scientific research directed towards the production of, for example, membranes for water desalination, drug-delivery devices, and nanosyringes. To develop these technologies it is crucial to understand and predict the equilibrium and transport properties of confined water. We present here a series of molecular dynamics simulation results conducted to understand the extent to which the presence of a few oxygenated active sites, modeled as carbonyls, affects the transport properties of confined water. The model for the carbon nanotube is not intended to be realistic. Its only purpose is to allow us to understand the effect of a few oxygenated sites on the transport properties of water confined in a narrow cylindrical pore, which is otherwise hydrophobic. At low hydration levels we found little, if any, water diffusion. The diffusion, which appears to be of the Fickian type for sufficiently large hydration levels, becomes faster as the number of confined water molecules increases, reaches a maximum, and slows as water fills the carbon nanotubes. We explain our findings on the basis of two collective motion mechanisms observed from the analysis of sequences of simulation snapshots. We term the two mechanisms 'cluster-breakage' and 'cluster-libration' mechanisms. We observe that the cluster-breakage mechanism produces longer displacements for the confined water molecules than the cluster-libration one, but deactivates as water fills the carbon nanotube. From a practical point of view, our results are particularly important for two reasons: (1) at low hydration levels the presence of only eight carbonyl groups can prevent the diffusion of water through (8, 8) carbon nanotubes; and (2) the extremely fast self-diffusion coefficients observed for water within narrow carbon nanotubes are significantly decreased in the presence of only a

Water self-diffusion through narrow oxygenated carbon nanotubes

International Nuclear Information System (INIS)

Striolo, Alberto

2007-01-01

The hydrophobic interior of carbon nanotubes, which is reminiscent of ion channels in cellular membranes, has inspired scientific research directed towards the production of, for example, membranes for water desalination, drug-delivery devices, and nanosyringes. To develop these technologies it is crucial to understand and predict the equilibrium and transport properties of confined water. We present here a series of molecular dynamics simulation results conducted to understand the extent to which the presence of a few oxygenated active sites, modeled as carbonyls, affects the transport properties of confined water. The model for the carbon nanotube is not intended to be realistic. Its only purpose is to allow us to understand the effect of a few oxygenated sites on the transport properties of water confined in a narrow cylindrical pore, which is otherwise hydrophobic. At low hydration levels we found little, if any, water diffusion. The diffusion, which appears to be of the Fickian type for sufficiently large hydration levels, becomes faster as the number of confined water molecules increases, reaches a maximum, and slows as water fills the carbon nanotubes. We explain our findings on the basis of two collective motion mechanisms observed from the analysis of sequences of simulation snapshots. We term the two mechanisms 'cluster-breakage' and 'cluster-libration' mechanisms. We observe that the cluster-breakage mechanism produces longer displacements for the confined water molecules than the cluster-libration one, but deactivates as water fills the carbon nanotube. From a practical point of view, our results are particularly important for two reasons: (1) at low hydration levels the presence of only eight carbonyl groups can prevent the diffusion of water through (8, 8) carbon nanotubes; and (2) the extremely fast self-diffusion coefficients observed for water within narrow carbon nanotubes are significantly decreased in the presence of only a few oxygenated active

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics.

Science.gov (United States)

Harvey, Michael G; Smith, Brian Tilston; Glenn, Travis C; Faircloth, Brant C; Brumfield, Robb T

2016-09-01

Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies. At shallow timescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species. We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture data sets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq data sets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of data sets and inferences with those of prior work. In RAD-Seq data sets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a data set to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among data sets and studies for the purpose of drawing general conclusions about the impact of

Carbon Nanotube Chopped Fiber for Enhanced Properties in Additive Manufacturing

Energy Technology Data Exchange (ETDEWEB)

Menchhofer, Paul A [ORNL; Lindahl, John M [ORNL; JohnsonPhD, DR Joseph E. [Nanocomp Technologies, Inc.

2016-06-06

Nanocomp Technologies, Inc. is working with Oak Ridge National Laboratory to develop carbon nanotube (CNT) composite materials and evaluate their use in additive manufacturing (3D printing). The first phase demonstrated feasibility and improvements for carbon nanotube (CNT)- acrylonitrile butadiene styrene (ABS) composite filaments use in additive manufacturing, with potential future work centering on further improvements. By focusing the initial phase on standard processing methods (developed mainly for the incorporation of carbon fibers in ABS) and characterization techniques, a basis of knowledge for the incorporation of CNTs in ABS was learned. The ability to understand the various processing variables is critical to the successful development of these composites. From the degradation effects on ABS (caused by excessive temperatures), to the length of time the ABS is in the melt state, to the order of addition of constituents, and also to the many possible mixing approaches, a workable flow sequence that addresses each processing step is critical to the final material properties. Although this initial phase could not deal with each of these variables in-depth, a future study is recommended that will build on the lessons learned for this effort.

Carbon Micronymphaea: Graphene on Vertically Aligned Carbon Nanotubes

Directory of Open Access Journals (Sweden)

Jong Won Choi

2013-01-01

Full Text Available This paper describes the morphology of carbon nanomaterials such as carbon nanotube (CNT, graphene, and their hybrid structure under various operating conditions during a one-step synthesis via plasma-enhanced chemical vapor deposition (PECVD. We focus on the synthetic aspects of carbon hybrid material composed of heteroepitaxially grown graphene on top of a vertical array of carbon nanotubes, called carbon micronymphaea. We characterize the structural features of this unique nanocomposite by uses of electron microscopy and micro-Raman spectroscopy. We observe carbon nanofibers, poorly aligned and well-aligned vertical arrays of CNT sequentially as the growth temperature increases, while we always discover the carbon hybrids, called carbon micronymphaea, at specific cooling rate of 15°C/s, which is optimal for the carbon precipitation from the Ni nanoparticles in this study. We expect one-pot synthesized graphene-on-nanotube hybrid structure poses great potential for applications that demand ultrahigh surface-to-volume ratios with intact graphitic nature and directional electronic and thermal transports.

Carbon Impact Analytics - Designing low carbon indices based on Carbon Impact Analytics indicators

International Nuclear Information System (INIS)

2016-01-01

Investors are increasingly exposed to carbon risks and now face the challenge of managing these risks and developing climate-resilient investment strategies. Carbon Impact Analytics (CIA), an innovative methodology for analyzing the full carbon impact of a portfolio or index, equips investors and asset managers with the tools necessary to reduce their climate-related risks but also to seize the opportunities offered by the ongoing energy transition. Investors, asset managers and other financial institutions may use CIA results to: - measure and manage risks, - optimize their contribution to the energy transition, - seize opportunities associated with climate change mitigation, - report on GHG emissions and savings (for regulatory purposes or voluntarily), - engage in dialogue with companies, - reallocate investment portfolios, - and build new low-carbon indices. In this report, Carbone 4 offers a detailed look into how CIA indicators can be used to either 1) reallocate an existing portfolio or index to achieve maximal carbon performance or 2) build new low carbon indices from the ground up, drawn from Carbone 4's ever-growing database of CIA-analyzed firms. Two main levers were used to optimize CIA output: 1. Sectorial reallocation: exclusion of fossil fuel-related sectors or insertion of low carbon pure players; 2. Intra-sectorial reallocation: best-in-class approach within a sector. Sectorial and intra-sectorial methods may be applied in conjunction with one another to maximize results. For example, a best-in-class + fossil fuel-free index may be constructed by first excluding the fossil fuel sector and then applying a CIA best-in-class approach to all remaining sectors. This report offers a detailed look into how CIA indicators can be used to rework portfolios or indices to maximize carbon performance or to build low carbon indices from the ground up. These methods are illustrated via two preliminary examples of indices designed by Carbone 4: the reallocated

Complete genome sequence of Paenibacillus riograndensis SBR5(T), a Gram-positive diazotrophic rhizobacterium.

Science.gov (United States)

Brito, Luciana Fernandes; Bach, Evelise; Kalinowski, Jörn; Rückert, Christian; Wibberg, Daniel; Passaglia, Luciane M; Wendisch, Volker F

2015-08-10

Paenibacillus riograndensis is a Gram-positive rhizobacterium which exhibits plant growth promoting activities. It was isolated from the rhizosphere of wheat grown in the state of Rio Grande do Sul, Brazil. Here we announce the complete genome sequence of P. riograndensis strain SBR5(T). The genome of P. riograndensis SBR5(T) consists of a circular chromosome of 7,893,056bps. The genome was finished and fully annotated, containing 6705 protein coding genes, 87 tRNAs and 27 rRNAs. The knowledge of the complete genome helped to explain why P. riograndensis SBR5(T) can grow with the carbon sources arabinose and mannitol, but not myo-inositol, and to explain physiological features such as biotin auxotrophy and antibiotic resistances. The genome sequence will be valuable for functional genomics and ecological studies as well as for application of P. riograndensis SBR5(T) as plant growth-promoting rhizobacterium. Copyright © 2015 Elsevier B.V. All rights reserved.

Carbon tetrachloride desorption from activated carbon

International Nuclear Information System (INIS)

Jonas, L.A.; Sansone, E.B.

1981-01-01

Carbon tetrachloride was desorbed from a granular activated carbon subsequent to its adsorption under various vapor exposure periods. The varied conditions of exposure resulted in a range of partially saturated carbon beds which, when followed by a constant flow rate for desorption, generated different forms of the desorbing concentration versus time curve. A method of analyzing the desorption curves is presented which permits extraction of the various desorbing rates from the different desorption and to relate this to the time required for such regeneration. The Wheeler desorption kinetic equation was used to calculate the pseudo first order desorption rate constant for the carbon. The desorption rate constant was found to increase monotonically with increasing saturation of the bed, permitting the calculation of the maximum desorption rate constant for the carbon at 100% saturation. The Retentivity Index of the carbon, defined as the dimensionless ratio of the adsorption to the desorption rate constant, was found to be 681

Multi-proxy approach for palaeoclimate reconstruction using a loess-palaeosol sequence from Süttő , Hungary

Science.gov (United States)

Thiel, Christine; Königer, Paul; Ostertag-Henning, Christian; Scheeder, Georg; Novothny, Ágnes; Horváth, Erzsébet; Wacha, Lara; Techmer, Astrid; Frechen, Manfred

2010-05-01

The loess-palaeosol sequence at Süttő , Hungary contains a high-resolution terrestrial archive of palaeoenvironmental changes. The sequence is about 20 m thick and overlies travertine which was dated using Uranium-series to 235-314 ka (Sierralta et al., in press). Imbedded with the loess are two greyish stratified horizons, three brownish steppe-like soils and a pedocomplex composed of a reddish-brown palaeosol covered by a chernozem. Detailed dating studies were carried out (Novothny et al, 2009, Novothny et al., in press) revealing more or less continuous sedimentation from marine isotope stage (MIS) 6 to MIS 2. High-resolution grain size and magnetic susceptibility data exist (Novothny et al., in prep.) which allow for palaeoenvironmental reconstructions. In addition to those data sets we analysed the carbon and oxygen isotopic composition of bulk carbonate, carbonate nodules, and organic material in order to get further insight into palaeoprecipitation and palaeoclimatic conditions. To strengthen the interpretation based on isotopic data, we examined biomarkers derived from land plants (long-chain n-alkanes) for both loess and palaeosols to add information on the vegetation changes. We will discuss the new results in comparison with the published data sets and highlight inherent problems of the individual approaches. Novothny, A., Frechen, M., Horváth, E., Wacha, L., Rolf, C., in prep. High resolution grain size and magnetic susceptibility record of the last glacial cycles in the Süttő loess section, Hungary. Quaternary International. Novothny, A., Frechen, M., Horváth, E., Krbetschek, M., Tsukamoto, S., in press. Infrared stimulated luminescence and radiofluorescence dating of aeolian sediments from Hungary. Quaternary Geochronology, doi:10.1016/j.quageo.2009.05.002. Novothny, A., Frechen, M., Horváth, E., Bradák, B., Oches, E. A., McCoy, W. D., Stevens, T., 2009a. Luminescence and amino acid racemisation chronology of the loess-paleosol sequence

Carbon-carbon mirrors for exoatmospheric and space applications

Science.gov (United States)

Krumweide, Duane E.; Wonacott, Gary D.; Woida, Patrick M.; Woida, Rigel Q.; Shih, Wei

2007-09-01

The cost and leadtime associated with beryllium has forced the MDA and other defense agencies to look for alternative materials with similar structural and thermal properties. The use of carbon-carbon material, specifically in optical components has been demonstrated analytically in prior SBIR work at San Diego Composites. Carbon-carbon material was chosen for its low in-plane and through-thickness CTE (athermal design), high specific stiffness, near-zero coefficient of moisture expansion, availability of material (specifically c-c honeycomb for lightweight substrates), and compatibility with silicon monoxide (SiO) and silicon dioxide (SiO II) coatings. Subsequent development work has produced shaped carbon-carbon sandwich substrates which have been ground, polished, coated and figured using traditional optical processing. Further development has also been done on machined monolithic carbon-carbon mirror substrates which have also been processed using standard optical finishing techniques.

A few Smarandache Integer Sequences

OpenAIRE

Ibstedt, Henry

2010-01-01

This paper deals with the analysis of a few Smarandache Integer Sequences which first appeared in Properties or the Numbers, F. Smarandache, University or Craiova Archives, 1975. The first four sequences are recurrence generated sequences while the last three are concatenation sequences.

Functional region prediction with a set of appropriate homologous sequences-an index for sequence selection by integrating structure and sequence information with spatial statistics

Science.gov (United States)

2012-01-01

Background The detection of conserved residue clusters on a protein structure is one of the effective strategies for the prediction of functional protein regions. Various methods, such as Evolutionary Trace, have been developed based on this strategy. In such approaches, the conserved residues are identified through comparisons of homologous amino acid sequences. Therefore, the selection of homologous sequences is a critical step. It is empirically known that a certain degree of sequence divergence in the set of homologous sequences is required for the identification of conserved residues. However, the development of a method to select homologous sequences appropriate for the identification of conserved residues has not been sufficiently addressed. An objective and general method to select appropriate homologous sequences is desired for the efficient prediction of functional regions. Results We have developed a novel index to select the sequences appropriate for the identification of conserved residues, and implemented the index within our method to predict the functional regions of a protein. The implementation of the index improved the performance of the functional region prediction. The index represents the degree of conserved residue clustering on the tertiary structure of the protein. For this purpose, the structure and sequence information were integrated within the index by the application of spatial statistics. Spatial statistics is a field of statistics in which not only the attributes but also the geometrical coordinates of the data are considered simultaneously. Higher degrees of clustering generate larger index scores. We adopted the set of homologous sequences with the highest index score, under the assumption that the best prediction accuracy is obtained when the degree of clustering is the maximum. The set of sequences selected by the index led to higher functional region prediction performance than the sets of sequences selected by other sequence

Incipiently drowned platform deposit in cyclic Ordovician shelf sequence: Lower Ordovician Chepultepec Formation, Virginia

Energy Technology Data Exchange (ETDEWEB)

Bova, J.A.; Read, J.F.

1983-03-01

The Chepultepec interval, 145 to 260 m (476 to 853 ft) thick, in Virginia contains the Lower Member up to 150 m (492 ft) thick, and the Upper Member, up to 85 m (279 ft) thick, of peritidal cyclic limestone and dolomite, and a Middle Member, up to 110 m (360 ft) thick, of subtidal limestone and bioherms, passing northwestward into cyclic facies. Calculated long term subsidence rates were 4 to 5 cm/1000 yr (mature passive margin rates), shelf gradients were 6 cm/km, and average duration of cycles was 140,00 years. Peritidal cyclic sequences are upward shallowing sequences of pellet-skeletal limestone, thrombolites, rippled calcisiltites and intraclast grainstone, and laminite caps. They formed by rapid transgression with apparent submergence increments averaging approximately 2 m (6.5 ft) in Lower Member and 3.5 m (11.4 ft), Upper Member. Deposition during Middle Member time was dominated by skeletal limestone-mudstone, calcisiltite with storm generated fining-upward sequences, and burrow-mixed units that were formed near fair-weather wave base, along with thrombolite bioherms. Locally, there are upward shallowing sequences, of basal wackestone/mudstone to calcisiltite to bioherm complexes (locally with erosional scalloped tops). Following each submergence, carbonate sedimentation was able to build to sea level prior to renewed submergence. Large submergence events caused tidal flats to be shifted far to the west, and they were unable to prograde out onto the open shelf because of insufficient time before subsidence was renewed, and because the open shelf setting inhibited tidal flat deposition. The Middle Member represents an incipiently drowned sequence that developed by repeated submergence events.

Developmental and Subcellular Organization of Single-Cell C₄ Photosynthesis in Bienertia sinuspersici Determined by Large-Scale Proteomics and cDNA Assembly from 454 DNA Sequencing.

Science.gov (United States)

Offermann, Sascha; Friso, Giulia; Doroshenk, Kelly A; Sun, Qi; Sharpe, Richard M; Okita, Thomas W; Wimmer, Diana; Edwards, Gerald E; van Wijk, Klaas J

2015-05-01

Kranz C4 species strictly depend on separation of primary and secondary carbon fixation reactions in different cell types. In contrast, the single-cell C4 (SCC4) species Bienertia sinuspersici utilizes intracellular compartmentation including two physiologically and biochemically different chloroplast types; however, information on identity, localization, and induction of proteins required for this SCC4 system is currently very limited. In this study, we determined the distribution of photosynthesis-related proteins and the induction of the C4 system during development by label-free proteomics of subcellular fractions and leaves of different developmental stages. This was enabled by inferring a protein sequence database from 454 sequencing of Bienertia cDNAs. Large-scale proteome rearrangements were observed as C4 photosynthesis developed during leaf maturation. The proteomes of the two chloroplasts are different with differential accumulation of linear and cyclic electron transport components, primary and secondary carbon fixation reactions, and a triose-phosphate shuttle that is shared between the two chloroplast types. This differential protein distribution pattern suggests the presence of a mRNA or protein-sorting mechanism for nuclear-encoded, chloroplast-targeted proteins in SCC4 species. The combined information was used to provide a comprehensive model for NAD-ME type carbon fixation in SCC4 species.

Carbon Sequestered, Carbon Displaced and the Kyoto Context

International Nuclear Information System (INIS)

Marland, G.; Schlamadinger, B.

1999-01-01

The integrated system that embraces forest management, forest products, and land-use change impacts the global carbon cycle - and hence the net emission of the greenhouse gas carbon dioxide - in four fundamental ways. Carbon is stored in living and dead biomass, carbon is stored in wood products and landfills, forest products substitute in the market place for products made from other materials, and forest harvests can be used wholly or partially to displace fossil fuels in the energy sector. Implementation of the Kyoto Protocol to the United Nations Framework Convention on Climate Change would result in the creation of international markets for carbon dioxide emissions credits, but the current Kyoto text does not treat all carbon identically. We have developed a carbon accounting model, GORCAM, to examine a variety of scenarios for land management and the production of forest products. In this paper we explore, for two simple scenarios of forest management, the carbon flows that occur and how these might be accounted for under the Kyoto text. The Kyoto protocol raises questions about what activities can result in emissions credits, which carbon reservoirs will be counted, who will receive the credits, and how much credit will be available? The Kyoto Protocol would sometimes give credits for carbon sequestered, but it would always give credits when fossil-fuel carbon dioxide emissions are displaced

Yeast genome sequencing:

DEFF Research Database (Denmark)

Piskur, Jure; Langkjær, Rikke Breinhold

2004-01-01

For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

Sequence Matters but How Exactly? A Method for Evaluating Activity Sequences from Data

Science.gov (United States)

Doroudi, Shayan; Holstein, Kenneth; Aleven, Vincent; Brunskill, Emma

2016-01-01

How should a wide variety of educational activities be sequenced to maximize student learning? Although some experimental studies have addressed this question, educational data mining methods may be able to evaluate a wider range of possibilities and better handle many simultaneous sequencing constraints. We introduce Sequencing Constraint…

Double polymer sheathed carbon nanotube supercapacitors show enhanced cycling stability

Science.gov (United States)

Zhao, Wenqi; Wang, Shanshan; Wang, Chunhui; Wu, Shiting; Xu, Wenjing; Zou, Mingchu; Ouyang, An; Cao, Anyuan; Li, Yibin

2015-12-01

Pseudo-materials are effective in boosting the specific capacitance of supercapacitors, but during service their degradation may also be very strong, causing reduced cycling stability. Here, we show that a carbon nanotube sponge grafted by two conventional pseudo-polymer layers in sequence can serve as a porous supercapacitor electrode with significantly enhanced cycling stability compared with single polymer grafting. Creating conformal polymer coatings on the nanotube surface and the resulting double-sheath configuration are important structural factors leading to the enhanced performance. Combining different polymers as double sheaths as reported here might be a potential route to circumvent the dilemma of pseudo-materials, and to simultaneously improve the capacitance and stability for various energy storage devices.Pseudo-materials are effective in boosting the specific capacitance of supercapacitors, but during service their degradation may also be very strong, causing reduced cycling stability. Here, we show that a carbon nanotube sponge grafted by two conventional pseudo-polymer layers in sequence can serve as a porous supercapacitor electrode with significantly enhanced cycling stability compared with single polymer grafting. Creating conformal polymer coatings on the nanotube surface and the resulting double-sheath configuration are important structural factors leading to the enhanced performance. Combining different polymers as double sheaths as reported here might be a potential route to circumvent the dilemma of pseudo-materials, and to simultaneously improve the capacitance and stability for various energy storage devices. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr05978j

Comprehensive Genetic Database of Expressed Sequence Tags for Coccolithophorids

Science.gov (United States)

Ranji, Mohammad; Hadaegh, Ahmad R.

Coccolithophorids are unicellular, marine, golden-brown, single-celled algae (Haptophyta) commonly found in near-surface waters in patchy distributions. They belong to the Phytoplankton family that is known to be responsible for much of the earth reproduction. Phytoplankton, just like plants live based on the energy obtained by Photosynthesis which produces oxygen. Substantial amount of oxygen in the earth's atmosphere is produced by Phytoplankton through Photosynthesis. The single-celled Emiliana Huxleyi is the most commonly known specie of Coccolithophorids and is known for extracting bicarbonate (HCO3) from its environment and producing calcium carbonate to form Coccoliths. Coccolithophorids are one of the world's primary producers, contributing about 15% of the average oceanic phytoplankton biomass to the oceans. They produce elaborate, minute calcite platelets (Coccoliths), covering the cell to form a Coccosphere and supplying up to 60% of the bulk pelagic calcite deposited on the sea floors. In order to understand the genetics of Coccolithophorid and the complexities of their biochemical reactions, we decided to build a database to store a complete profile of these organisms' genomes. Although a variety of such databases currently exist, (http://www.geneservice.co.uk/home/) none have yet been developed to comprehensively address the sequencing efforts underway by the Coccolithophorid research community. This database is called CocooExpress and is available to public (http://bioinfo.csusm.edu) for both data queries and sequence contribution.

Mapping sequences by parts

Directory of Open Access Journals (Sweden)

Guziolowski Carito

2007-09-01

Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

Synthesis and Characterization Carbon Nanotubes Doped Carbon Aerogels

Science.gov (United States)

Xu, Yuelong; Yan, Meifang; Liu, Zhenfa

2017-12-01

Polycondensation of phloroglucinol, resorcinol and formaldehyde with carbon nanotube (CNT) as the additives, using sodium carbonate as the catalyst, leads to the formation of CNT - doped carbon aerogels. The structure of carbon aerogels (CAs) with carbon nanotubes (CNTs) were characterized by X-ray diffraction and scanning electron microscopy. The specific surface area, pore size distribution and pore volume were measured by surface area analyzer. The results show that when the optimum doping dosage is 5%, the specific surface area of CNT - doped carbon aerogel is up to 665 m2 g-1 and exhibit plentiful mesoporous.

Carbon Management In the Post-Cap-and-Trade Carbon Economy

Science.gov (United States)

DeGroff, F. A.

2013-12-01

This abstract outlines an economic model that integrates carbon externalities seamlessly into the national and international economies. The model incorporates a broad carbon metric used to value all carbon in the biosphere, as well as all transnational commerce. The model minimizes the cost associated with carbon management, and allows for the variation in carbon avidity between jurisdictions. When implemented over time, the model reduces the deadweight loss while minimizing social cost, thus maximizing the marginal social benefit commonly associated with Pigouvian taxes. Once implemented, the model provides a comprehensive economic construct for governments, industry and consumers to efficiently weigh the cost of carbon, and effectively participate in helping to reduce their direct and indirect use of carbon, while allowing individual jurisdictions to decide their own carbon value, without the need for explicit, express agreement of all countries. The model uses no credits, requires no caps, and matches climate changing behavior to costs. The steps to implement the model for a particular jurisdiction are: 1) Define the Carbon Metric to value changes in Carbon Quality. 2) Apply the Carbon Metric to assess the Carbon Toll a) for all changes in Carbon Quality and b) for imports and exports. This economic model has 3 clear advantages. 1) The carbon pricing and cost scheme use existing and generally accepted accounting methodologies to ensure the veracity and verifiability of carbon management efforts with minimal effort and expense using standard auditing protocols. Implementing this economic model will not require any special training, tools, or systems for any entity to achieve their minimum carbon target goals within their jurisdictional framework. 2) Given the spectrum of carbon affinities worldwide, the model recognizes and provides for flexible carbon pricing regimes, but does not penalize domestic carbon-consuming producers subject to imports from exporters in

Measurement of carbon capture efficiency and stored carbon leakage

Science.gov (United States)

Keeling, Ralph F.; Dubey, Manvendra K.

2013-01-29

Data representative of a measured carbon dioxide (CO.sub.2) concentration and of a measured oxygen (O.sub.2) concentration at a measurement location can be used to determine whether the measured carbon dioxide concentration at the measurement location is elevated relative to a baseline carbon dioxide concentration due to escape of carbon dioxide from a source associated with a carbon capture and storage process. Optionally, the data can be used to quantify a carbon dioxide concentration increase at the first location that is attributable to escape of carbon dioxide from the source and to calculate a rate of escape of carbon dioxide from the source by executing a model of gas-phase transport using at least the first carbon dioxide concentration increase. Related systems, methods, and articles of manufacture are also described.

From Sequence to Morphology - Long-Range Correlations in Complete Sequenced Genomes

NARCIS (Netherlands)

T.A. Knoch (Tobias)

2004-01-01

textabstractThe largely unresolved sequential organization, i.e. the relations within DNA sequences, and its connection to the three-dimensional organization of genomes was investigated by correlation analyses of completely sequenced chromosomes from Viroids, Archaea, Bacteria, Arabidopsis

Carbon sequestration potential of forest land: Management for products and bioenergy versus preservation

International Nuclear Information System (INIS)

Van Deusen, P.

2010-01-01

A 40 year projection of potential carbon sequestration is based on USDA Forest Service Forest Inventory and Analysis (FIA) data from the state of Georgia. The objective is to compare carbon sequestration under a sustainable management strategy versus a preservation strategy. FIA plots are projected ahead in time with hotdeck matching. This matches each subject plot with another plot from the database that represents the subject plot at a future time. The matched plot sequences are used to provide input data to a harvest scheduling program to generate a management strategy for the state. The sequestration from the management strategy is compared with a preservation strategy that involves no harvesting. Harvested wood is assumed to go into products with various half life decay rates. Carbon sequestration is increased as increasing proportions go into wood for energy, which is treated like a product with an infinite half life. Therefore, the harvested carbon does not return immediately to the atmosphere. Public land and land close to cities is assumed to be unavailable, and all other private land is assumed to be accessible. The results are presented as gigatonnes of CO 2 equivalent to make them directly comparable to US annual carbon emissions. The conclusion is that forest management will sequester more above-ground carbon than preservation over a 40 year period if the wood is used for products with an average half life greater than 5 years.

Isolation and characterization of Sulfurospirillum carboxydovorans sp. nov., a new microaerophilic carbon monoxide oxidizing epsilon Proteobacterium.

Science.gov (United States)

Jensen, Anders; Finster, Kai

2005-05-01

A new microaerophilic, Gram-negative, motile, 2-3 microm long and 0.3 microm wide, vibrioid to spirillum-shaped, CO oxidizing bacterium, designated strain MV, isolated from marine sediment (The North Sea) is described. Strain MV was able to couple the oxidation of CO to the reduction of elemental sulphur, DMSO and thiosulphate. Growth occurred with up to 100% (v/v) CO in the headspace. Acetate was needed as carbon source. No growth on CO was observed with nitrate and selenate as electron acceptor. Sulphite, elemental sulphur, DMSO, thiosulphate, nitrate, nitrite, perchloroethylene, arsenate and selenate were used as electron acceptors with pyruvate as energy and carbon source. Microaerophilic growth was observed. In non-agitated cultures growth occurred at atmospheric oxygen concentrations in the headspace. Hydrogen (with acetate as carbon source), formate (with acetate as carbon source), pyruvate, lactate, succinate, fumarate, malate alpha-ketoglutaric acid, aspartate and yeast extract (1% (w/v)) supported growth with nitrate as electron acceptor. Fumarate and malate were fermented. Vitamins were not required for growth. The strain was cytochrome C oxidase and catalase positive. The DNA mol G+C content was 30.5%. 16S rRNA gene sequence comparison showed that strain MV grouped within the genus Sulfurospirillum with Sulfurospirillum arcachonense (sequence similarity 98.3%) as closest relative. The relative DNA-DNA relatedness between strain MV and S. arcachonense was 33.1%. Based on a detailed phenotypic and phylogenetic analysis, inclusion of strain MV in the genus Sulfurospirillum as a well separated new species is proposed. As species name we propose Sulfurospirillum carboxydovorans. The type strain is strain MV (ATCC BAA-937 = DSM 16295, GenBank accession number: AY740528).

Solvation behavior of carbonate-based electrolytes in sodium ion batteries.

Science.gov (United States)

Cresce, Arthur V; Russell, Selena M; Borodin, Oleg; Allen, Joshua A; Schroeder, Marshall A; Dai, Michael; Peng, Jing; Gobet, Mallory P; Greenbaum, Steven G; Rogers, Reginald E; Xu, Kang

2016-12-21

Sodium ion batteries are on the cusp of being a commercially available technology. Compared to lithium ion batteries, sodium ion batteries can potentially offer an attractive dollar-per-kilowatt-hour value, though at the penalty of reduced energy density. As a materials system, sodium ion batteries present a unique opportunity to apply lessons learned in the study of electrolytes for lithium ion batteries; specifically, the behavior of the sodium ion in an organic carbonate solution and the relationship of ion solvation with electrode surface passivation. In this work the Li + and Na + -based solvates were characterized using electrospray mass spectrometry, infrared and Raman spectroscopy, 17 O, 23 Na and pulse field gradient double-stimulated-echo pulse sequence nuclear magnetic resonance (NMR), and conductivity measurements. Spectroscopic evidence demonstrate that the Li + and Na + cations share a number of similar ion-solvent interaction trends, such as a preference in the gas and liquid phase for a solvation shell rich in cyclic carbonates over linear carbonates and fluorinated carbonates. However, quite different IR spectra due to the PF 6 - anion interactions with the Na + and Li + cations were observed and were rationalized with the help of density functional theory (DFT) calculations that were also used to examine the relative free energies of solvates using cluster - continuum models. Ion-solvent distances for Na + were longer than Li + , and Na + had a greater tendency towards forming contact pairs compared to Li + in linear carbonate solvents. In tests of hard carbon Na-ion batteries, performance was not well correlated to Na + solvent preference, leading to the possibility that Na + solvent preference may play a reduced role in the passivation of anode surfaces and overall Na-ion battery performance.

Biomolecule Sequencer: Next-Generation DNA Sequencing Technology for In-Flight Environmental Monitoring, Research, and Beyond

Science.gov (United States)

Smith, David J.; Burton, Aaron; Castro-Wallace, Sarah; John, Kristen; Stahl, Sarah E.; Dworkin, Jason Peter; Lupisella, Mark L.

2016-01-01

On the International Space Station (ISS), technologies capable of rapid microbial identification and disease diagnostics are not currently available. NASA still relies upon sample return for comprehensive, molecular-based sample characterization. Next-generation DNA sequencing is a powerful approach for identifying microorganisms in air, water, and surfaces onboard spacecraft. The Biomolecule Sequencer payload, manifested to SpaceX-9 and scheduled on the Increment 4748 research plan (June 2016), will assess the functionality of a commercially-available next-generation DNA sequencer in the microgravity environment of ISS. The MinION device from Oxford Nanopore Technologies (Oxford, UK) measures picoamp changes in electrical current dependent on nucleotide sequences of the DNA strand migrating through nanopores in the system. The hardware is exceptionally small (9.5 x 3.2 x 1.6 cm), lightweight (120 grams), and powered only by a USB connection. For the ISS technology demonstration, the Biomolecule Sequencer will be powered by a Microsoft Surface Pro3. Ground-prepared samples containing lambda bacteriophage, Escherichia coli, and mouse genomic DNA, will be launched and stored frozen on the ISS until experiment initiation. Immediately prior to sequencing, a crew member will collect and thaw frozen DNA samples, connect the sequencer to the Surface Pro3, inject thawed samples into a MinION flow cell, and initiate sequencing. At the completion of the sequencing run, data will be downlinked for ground analysis. Identical, synchronous ground controls will be used for data comparisons to determine sequencer functionality, run-time sequence, current dynamics, and overall accuracy. We will present our latest results from the ISS flight experiment the first time DNA has ever been sequenced in space and discuss the many potential applications of the Biomolecule Sequencer for environmental monitoring, medical diagnostics, higher fidelity and more adaptable Space Biology Human

Pairwise Sequence Alignment Library

Energy Technology Data Exchange (ETDEWEB)

2015-05-20

Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation.

Directory of Open Access Journals (Sweden)

Flavia Vischi Winck

Full Text Available The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO2], a carbon concentrating mechanism (CCM is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1 gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF and transcription regulator (TR genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO 2 response regulator 1 and Lcr2 (Low-CO2 response regulator 2, may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome

The Crc protein inhibits the production of polyhydroxyalkanoates in Pseudomonas putida under balanced carbon/nitrogen growth conditions.

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La Rosa, Ruggero; de la Peña, Fernando; Prieto, María Axiliadora; Rojo, Fernando

2014-01-01

Pseudomonas putida synthesizes polyhydroxyalkanoates (PHAs) as storage compounds. PHA synthesis is more active when the carbon source is in excess and the nitrogen source is limiting, but can also occur at a lower rate under balanced carbon/nitrogen ratios. This work shows that PHA synthesis is controlled by the Crc global regulator, a protein that optimizes carbon metabolism by inhibiting the expression of genes involved in the use of non-preferred carbon sources. Crc acts post-transcriptionally. The mRNAs of target genes contain characteristic catabolite activity (CA) motifs near the ribosome binding site. Sequences resembling CA motifs can be predicted for the phaC1 gene, which codes for a PHA polymerase, and for phaI and phaF, which encode proteins associated to PHA granules. Our results show that Crc inhibits the translation of phaC1 mRNA, but not that of phaI or phaF, reducing the amount of PHA accumulated in the cell. Crc inhibited PHA synthesis during exponential growth in media containing a balanced carbon/nitrogen ratio. No inhibition was seen when the carbon/nitrogen ratio was imbalanced. This extends the role of Crc beyond that of controlling the hierarchical utilization of carbon sources and provides a link between PHA synthesis and the global regulatory networks controlling carbon flow. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Neutron scattering investigation of carbon/carbon composites

International Nuclear Information System (INIS)

Prem, M.; Krexner, G.; Peterlik, H.

2005-01-01

Full text: Carbon/Carbon (C/C) composites, built up from bi-directionally woven fabrics from PAN based carbon fibers, pre-impregnated with phenolic resin followed by pressure curing and carbonization at 1000 o C and a final heat treatment at either 1800 o C or 2400 o C, were investigated by means of small-angle as well as wideangle elastic neutron scattering. Sample orientations arranging the carbon fibers parallel and perpendicular to the incoming beam were examined. Structural features of the composites, i.e. of the fibers as well as the inherently existing pores, are presented and the influence of the heat treatment on the structural properties is discussed. (author)

Sedimentary mode and reservoir distribution of the Cambrian carbonate & evaporate paragenesis system in the Sichuan Basin

Directory of Open Access Journals (Sweden)

Anna Xu

2016-11-01

Full Text Available The Cambrian carbonate & evaporite paragenesis system in the Sichuan Basin is made up of the Longwangmiao, Gaotai and Xixiangchi Fms. So far, great breakthrough has been made only in the Longwangmiao Fm instead of the latter two, and the Anyue Gasfield was discovered in the center of this basin. In this paper, therefore, the Cambrian carbonate & evaporite paragenesis system in the Sichuan Basin was analyzed in terms of its structural–sedimentary setting, sequence stratigraphic framework, sedimentary facies and the distribution of evaporites by using various geologic, logging and seismic data. Then, the geological model of sedimentary facies was established and the distribution range of favorable reservoirs was predicted. Based on these studies, the following results are obtained. Firstly, the palaeotectonic framework is characterized by the style of “one depression between two uplifts” in the setting of a large SE dipping slope, and the stratigraphic filling is in the structure of “onlapping at the bottom and truncation at the top” which is thin in the west and thick in the east. Secondly, three third-order sequence cycles which, on the whole, become shallow upward are developed from bottom to top, and gypsum-salt rocks are mainly located at the high system tract (HST of third-order sequences and concentrated in the Wanzhou–Yibin sag. Thirdly, the geological model of sedimentary facies is composed of three major sedimentary structural layers from bottom to top, namely the evaporative carbonate ramp, the evaporative diamictic restricted platform and the evaporative restricted platform. The sedimentary environment changes from the open to the closed and the penesaline for a long time, and then back to the open. The distribution of shoals changes from the pattern of “dual banks” in a large area to more scattered shoals and banded shoals, while the evaporative lagoon and tidal flat shrink. Fourthly, the reservoir distribution is

Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.

Directory of Open Access Journals (Sweden)

Stephan Pabinger

Full Text Available Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM. Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage

Inference of Interactions in Cyanobacterial-Heterotrophic Co-Cultures via Transcriptome Sequencing

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Beliaev, Alex S.; Romine, Margaret F.; Serres, Margaret; Bernstein, Hans C.; Linggi, Bryan E.; Markillie, Lye Meng; Isern, Nancy G.; Chrisler, William B.; Kucek, Leo A.; Hill, Eric A.; Pinchuk, Grigoriy; Bryant, Donald A.; Wiley, H. S.; Fredrickson, Jim K.; Konopka, Allan

2014-04-29

We employed deep sequencing technology to identify transcriptional adaptation of the euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002 and the marine facultative aerobe Shewanella putrefaciens W3-18-1 to growth in a co-culture and infer the effect of carbon flux distributions on photoautotroph-heterotroph interactions. The overall transcriptome response of both organisms to co-cultivation was shaped by their respective physiologies and growth constraints. Carbon limitation resulted in the expansion of metabolic capacities which was manifested through the transcriptional upregulation of transport and catabolic pathways. While growth coupling occurred via lactate oxidation or secretion of photosynthetically fixed carbon, there was evidence of specific metabolic interactions between the two organisms. On one hand, the production and excretion of specific amino acids (methionine and alanine) by the cyanobacterium correlated with the putative downregulation of the corresponding biosynthetic machinery of Shewanella W3-18-1. On the other hand, the broad and consistent decrease of mRNA levels for many Fe-regulated Synechococcus 7002 genes during co-cultivation suggested increased Fe availability as well as more facile and energy-efficient mechanisms for Fe acquisition by the cyanobacterium. Furthermore, evidence pointed at potentially novel interactions between oxygenic photoautotrophs and heterotrophs related to the oxidative stress response as transcriptional patterns suggested that Synechococcus 7002 rather than Shewanella W3-18-1 provided scavenging functions for reactive oxygen species under co-culture conditions. This study provides an initial insight into the complexity of photoautotrophic-heterotrophic interactions and brings new perspectives of their role in the robustness and stability of the association.

DNA Sequencing by Capillary Electrophoresis

Science.gov (United States)

Karger, Barry L.; Guttman, Andras

2009-01-01

Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

HIV Sequence Compendium 2015

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Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2015-10-05

This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

PN Sequence Preestimator Scheme for DS-SS Signal Acquisition Using Block Sequence Estimation

Directory of Open Access Journals (Sweden)

Sang Kyu Park

2005-03-01

Full Text Available An m-sequence (PN sequence preestimator scheme for direct-sequence spread spectrum (DS-SS signal acquisition by using block sequence estimation (BSE is proposed and analyzed. The proposed scheme consists of an estimator and a verifier which work according to the PN sequence chip clock, and provides not only the enhanced chip estimates with a threshold decision logic and one-chip error correction among the first m received chips, but also the reliability check of the estimates with additional decision logic. The probabilities of the estimator and verifier operations are calculated. With these results, the detection, the false alarm, and the missing probabilities of the proposed scheme are derived. In addition, using a signal flow graph, the average acquisition time is calculated. The proposed scheme can be used as a preestimator and easily implemented by changing the internal signal path of a generally used digital matched filter (DMF correlator or any other correlator that has a lot of sampling data memories for sampled PN sequence. The numerical results show rapid acquisition performance in a relatively good CNR.

Porous carbons prepared by direct carbonization of MOFs for supercapacitors

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Yan, Xinlong; Li, Xuejin; Yan, Zifeng; Komarneni, Sridhar

2014-07-01

Three porous carbons were prepared by direct carbonization of HKUST-1, MOF-5 and Al-PCP without additional carbon precursors. The carbon samples obtained by carbonization at 1073 K were characterized by XRD, TEM and N2 physisorption techniques followed by testing for electrochemical performance. The BET surface areas of the three carbons were in the range of 50-1103 m2/g. As electrode materials for supercapacitor, the MOF-5 and Al-PCP derived carbons displayed the ideal capacitor behavior, whereas the HKUST-1 derived carbon showed poor capacitive behavior at various sweep rates and current densities. Among those carbon samples, Al-PCP derived carbons exhibited highest specific capacitance (232.8 F/g) in 30% KOH solution at the current density of 100 mA/g.

GuiTope: an application for mapping random-sequence peptides to protein sequences.

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Halperin, Rebecca F; Stafford, Phillip; Emery, Jack S; Navalkar, Krupa Arun; Johnston, Stephen Albert

2012-01-03

Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task. GuiTope provides a graphical user interface for aligning peptide sequences to protein sequences. All alignment parameters are accessible to the user including the ability to specify the amino acid frequency in the peptide library; these frequencies often differ significantly from those assumed by popular alignment programs. It also includes a novel feature to align di-peptide inversions, which we have found improves the accuracy of antibody epitope prediction from peptide microarray data and shows utility in analyzing phage display datasets. Finally, GuiTope can randomly select peptides from a given library to estimate a null distribution of scores and calculate statistical significance. GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features, ability to search a database, and statistical significance of results. The software is available as an executable (for PC) at http://www.immunosignature.com/software and ongoing updates and source code will be available at sourceforge.net.

GuiTope: an application for mapping random-sequence peptides to protein sequences

Directory of Open Access Journals (Sweden)

Halperin Rebecca F

2012-01-01

Full Text Available Abstract Background Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task. Results GuiTope provides a graphical user interface for aligning peptide sequences to protein sequences. All alignment parameters are accessible to the user including the ability to specify the amino acid frequency in the peptide library; these frequencies often differ significantly from those assumed by popular alignment programs. It also includes a novel feature to align di-peptide inversions, which we have found improves the accuracy of antibody epitope prediction from peptide microarray data and shows utility in analyzing phage display datasets. Finally, GuiTope can randomly select peptides from a given library to estimate a null distribution of scores and calculate statistical significance. Conclusions GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features, ability to search a database, and statistical significance of results. The software is available as an executable (for PC at http://www.immunosignature.com/software and ongoing updates and source code will be available at sourceforge.net.

Targeted sequencing of plant genomes

Science.gov (United States)

Mark D. Huynh

2014-01-01

Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

Repdigits in k-Lucas sequences

Indian Academy of Sciences (India)

57(2) 2000 243-254) proved that 11 is the largest number with only one distinct digit (the so-called repdigit) in the sequence ( L n ( 2 ) ) n . In this paper, we address a similar problem in the family of -Lucas sequences. We also show that the -Lucas sequences have similar properties to those of -Fibonacci sequences ...

Radiation damage in carbon-carbon composites: Structure and property effects

International Nuclear Information System (INIS)

Burchell, T.D.

1995-01-01

Carbon-carbon composites are an attractive choice for fusion reactor plasma facing components because of their low atomic number, superior thermal shock resistance, and low neutron activation. Next generation tokamak reactors such as the International Thermonuclear Experimental Reactor (ITER), will require high thermal conductivity carbon-carbon composites and other materials, such as beryllium, to protect their plasma facing components from the anticipated high heat fluxes. Moreover, ignition machines such as ITER will produce a large neutron flux. Consequently, the influence of neutron damage on the structure and properties of carbon-carbon composite materials must be evaluated. Data from two irradiation experiments are reported and discussed here. Carbon-carbon composite materials were irradiated in target capsules in the High Flux Isotope Reactor (HAIR) at Oak Ridge National Laboratory (ORAL). A peak damage dose of 4.7 displacements per atom (da) at an irradiation temperature of ∼600 degrees C was attained. The carbon materials irradiated here included unidirectional, two- directional, and three-directional carbon-carbon composites. Irradiation induced dimensional changes are reported for the materials and related to single crystal dimensional changes through fiber and composite structural models. Moreover, carbon-carbon composite material dimensional changes are discussed in terms of their architecture, fiber type, and graphitization temperature. Neutron irradiation induced reductions in the thermal conductivity of two, three-directional carbon-carbon composites are reported, and the recovery of thermal conductivity due to thermal annealing is demonstrated. Irradiation induced strength changes are reported for several carbon-carbon composite materials and are explained in terms of in-crystal and composite structural effects

White dwarf stars with carbon atmospheres.

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Dufour, P; Liebert, J; Fontaine, G; Behara, N

2007-11-22

White dwarfs represent the endpoint of stellar evolution for stars with initial masses between approximately 0.07 and 8-10, where is the mass of the Sun (more massive stars end their life as either black holes or neutron stars). The theory of stellar evolution predicts that the majority of white dwarfs have a core made of carbon and oxygen, which itself is surrounded by a helium layer and, for approximately 80 per cent of known white dwarfs, by an additional hydrogen layer. All white dwarfs therefore have been traditionally found to belong to one of two categories: those with a hydrogen-rich atmosphere (the DA spectral type) and those with a helium-rich atmosphere (the non-DAs). Here we report the discovery of several white dwarfs with atmospheres primarily composed of carbon, with little or no trace of hydrogen or helium. Our analysis shows that the atmospheric parameters found for these stars do not fit satisfactorily in any of the currently known theories of post-asymptotic giant branch evolution, although these objects might be the cooler counterpart of the unique and extensively studied PG 1159 star H1504+65 (refs 4-7). These stars, together with H1504+65, might accordingly form a new evolutionary sequence that follows the asymptotic giant branch.

Rivers of Carbon: Carbon Fluxes in a Watershed Context

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Wohl, E.; Tom, B.; Hovius, N.

2017-12-01

Research within the past decade has identified the roles of diverse terrestrial processes in mobilizing terrestrial carbon from bedrock, soil, and vegetation and in redistributing this carbon among the atmosphere, biota, geosphere, and oceans. Rivers are central to carbon redistribution, serving as the primary initial receptor of mobilized terrestrial carbon, as well as governing the proportions of carbon sequestered within sediment, transported to oceans, or released to the atmosphere. We use a riverine carbon budget to examine how key questions regarding carbon dynamics can be addressed across diverse spatial and temporal scales from sub-meter areas over a few hours on a single gravel bar to thousands of square kilometers over millions of years across an entire large river network. The portion of the budget applying to the active channel(s) takes the form of ,in which Cs is organic carbon storage over time t. Inputs are surface and subsurface fluxes from uplands (CIupl) and the floodplain (CIfp), including fossil, soil, and biospheric organic carbon; surface and subsurface fluxes of carbon dioxide to the channel (CICO2); and net primary productivity in the channel (CINPP). Outputs occur via respiration within the channel and carbon dioxide emissions (COgas) and fluxes of dissolved and particulate organic carbon to the floodplain and downstream portions of the river network (COriver). The analogous budget for the floodplain portion of a river corridor is .

Profile of microbial communities on carbonate stones of the medieval church of San Leonardo di Siponto (Italy) by Illumina-based deep sequencing.

Science.gov (United States)

Chimienti, Guglielmina; Piredda, Roberta; Pepe, Gabriella; van der Werf, Inez Dorothé; Sabbatini, Luigia; Crecchio, Carmine; Ricciuti, Patrizia; D'Erchia, Anna Maria; Manzari, Caterina; Pesole, Graziano

2016-10-01

Comprehensive studies of the biodiversity of the microbial epilithic community on monuments may provide critical insights for clarifying factors involved in the colonization processes. We carried out a high-throughput investigation of the communities colonizing the medieval church of San Leonardo di Siponto (Italy) by Illumina-based deep sequencing. The metagenomic analysis of sequences revealed the presence of Archaea, Bacteria, and Eukarya. Bacteria were Actinobacteria, Proteobacteria, Bacteroidetes, Cyanobacteria, Chloroflexi, Firmicutes and Candidatus Saccharibacteria. The predominant phylum was Actinobacteria, with the orders Actynomycetales and Rubrobacteriales, represented by the genera Pseudokineococcus, Sporichthya, Blastococcus, Arthrobacter, Geodermatophilus, Friedmanniella, Modestobacter, and Rubrobacter, respectively. Cyanobacteria sequences showing strong similarity with an uncultured bacterium sequence were identified. The presence of the green algae Oocystaceae and Trebuxiaceae was revealed. The microbial diversity was explored at qualitative and quantitative levels, evaluating the richness (the number of operational taxonomic units (OTUs)) and the abundance of reads associated with each OTU. The rarefaction curves approached saturation, suggesting that the majority of OTUs were recovered. The results highlighted a structured community, showing low diversity, made up of extremophile organisms adapted to desiccation and UV radiation. Notably, the microbiome appeared to be composed not only of microorganisms possibly involved in biodeterioration but also of carbonatogenic bacteria, such as those belonging to the genus Arthrobacter, which could be useful in bioconservation. Our investigation demonstrated that molecular tools, and in particular the easy-to-run next-generation sequencing, are powerful to perform a microbiological diagnosis in order to plan restoration and protection strategies.

Solid phase extraction of uranium(VI) onto benzoylthiourea-anchored activated carbon

Energy Technology Data Exchange (ETDEWEB)

Zhao Yongsheng; Liu Chunxia; Feng Miao; Chen Zhen; Li Shuqiong; Tian Gan; Wang Li; Huang Jingbo [College of Chemistry, Sichuan University, 29 Wangjiang Lu, Chengdu, 610064, Sichuan (China); Li Shoujian, E-mail: sjli000616@scu.edu.cn [College of Chemistry, Sichuan University, 29 Wangjiang Lu, Chengdu, 610064, Sichuan (China)

2010-04-15

A new solid phase extractant selective for uranium(VI) based on benzoylthiourea anchored to activated carbon was developed via hydroxylation, amidation and reaction with benzoyl isothiocyanate in sequence. Fourier transform infrared spectroscopy and total element analysis proved that benzoylthiourea had been successfully grafted to the surface of the activated carbon, with a loading capacity of 1.2 mmol benzoylthiourea per gram of activated carbon. The parameters that affect the uranium(VI) sorption, such as contact time, solution pH, initial uranium(VI) concentration, adsorbent dose and temperature, have been investigated. Results have been analyzed by Langmuir and Freundlich isotherm; the former was more suitable to describe the sorption process. The maximum sorption capacity (82 mg/g) for uranium(VI) was obtained at experimental conditions. The rate constant for the uranium sorption by the as-synthesized extractant was 0.441 min{sup -1} from the first order rate equation. Thermodynamic parameters ({Delta}H{sup 0} = -46.2 kJ/mol; {Delta}S{sup 0} = -98.0 J/mol K; {Delta}G{sup 0} = -17.5 kJ/mol) showed the adsorption of an exothermic process and spontaneous nature, respectively. Additional studies indicated that the benzoylthiourea-anchored activated carbon (BT-AC) selectively sorbed uranyl ions in the presence of competing ions, Na{sup +}, Co{sup 2+}, Sr{sup 2+}, Cs{sup +} and La{sup 3+}.

Thermal Oxidation of a Carbon Condensate Formed in High-Frequency Carbon and Carbon-Nickel Plasma Flow

Science.gov (United States)

Churilov, G. N.; Nikolaev, N. S.; Cherepakhin, A. V.; Dudnik, A. I.; Tomashevich, E. V.; Trenikhin, M. V.; Bulina, N. G.

2018-02-01

We have reported on the comparative characteristics of thermal oxidation of a carbon condensate prepared by high-frequency arc evaporation of graphite rods and a rod with a hollow center filled with nickel powder. In the latter case, along with different forms of nanodisperse carbon, nickel particles with nickel core-carbon shell structures are formed. It has been found that the processes of the thermal oxidation of carbon condensates with and without nickel differ significantly. Nickel particles with the carbon shell exhibit catalytic properties with respect to the oxidation of nanosized carbon structures. A noticeable difference between the temperatures of the end of the oxidation process for various carbon nanoparticles and nickel particles with the carbon shell has been established. The study is aimed at investigations of the effect of nickel nanoparticles on the dynamics of carbon condensate oxidation upon heating in the argon-oxygen flow.

Graphitization in Carbon MEMS and Carbon NEMS

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Sharma, Swati

Carbon MEMS (CMEMS) and Carbon NEMS (CNEMS) are an emerging class of miniaturized devices. Due to the numerous advantages such as scalable manufacturing processes, inexpensive and readily available precursor polymer materials, tunable surface properties and biocompatibility, carbon has become a preferred material for a wide variety of future sensing applications. Single suspended carbon nanowires (CNWs) integrated on CMEMS structures fabricated by electrospinning of SU8 photoresist on photolithographially patterned SU8 followed by pyrolysis are utilized for understanding the graphitization process in micro and nano carbon materials. These monolithic CNW-CMEMS structures enable the fabrication of very high aspect ratio CNWs of predefined length. The CNWs thus fabricated display core---shell structures having a graphitic shell with a glassy carbon core. The electrical conductivity of these CNWs is increased by about 100% compared to glassy carbon as a result of enhanced graphitization. We explore various tunable fabrication and pyrolysis parameters to improve graphitization in the resulting CNWs. We also suggest gas-sensing application of the thus fabricated single suspended CNW-CMEMS devices by using the CNW as a nano-hotplate for local chemical vapor deposition. In this thesis we also report on results from an optimization study of SU8 photoresist derived carbon electrodes. These electrodes were applied to the simultaneous detection of traces of Cd(II) and Pb(II) through anodic stripping voltammetry and detection limits as low as 0.7 and 0.8 microgL-1 were achieved. To further improve upon the electrochemical behavior of the carbon electrodes we elucidate a modified pyrolysis technique featuring an ultra-fast temperature ramp for obtaining bubbled porous carbon from lithographically patterned SU8. We conclude this dissertation by suggesting the possible future works on enhancing graphitization as well as on electrochemical applications

Crystallization, characterization and preliminary X-ray crystallographic analysis of GK2848, a putative carbonic anhydrase of Geobacillus kaustophilus

International Nuclear Information System (INIS)

Ragunathan, Preethi; Raghunath, Gokul; Kuramitsu, Seiki; Yokoyama, Shigeyuki; Kumarevel, Thirumananseri; Ponnuraj, Karthe

2013-01-01

The expression, purification, characterization and crystallization of GK2848, a carbonic anhydrase from G. kaustophilus, are described. The crystals diffracted to a resolution of 2.70 Å. GK2848, a hypothetical protein from the thermophilic organism Geobacillus kaustophilus, was cloned and overexpressed in Escherichia coli. The protein was purified to homogeneity using Ni–NTA affinity-column and gel-filtration chromatography. The purified protein was crystallized using the sitting-drop vapour-diffusion method. The crystals diffracted to a resolution of 2.70 Å and belonged to the orthorhombic space group P2 1 2 1 2. GK2848 bears sequence homology to carbonic anhydrases of various bacterial species, indicating that it belongs to the carbonic anhydrase family of proteins. A subsequent carbonic anhydrase activity assay of GK2848 using the Wilbur–Anderson method confirmed its function as a carbonic anhydrase. A preliminary structure solution was obtained by molecular replacement using MOLREP. Mutation and biochemical characterization of the protein are in progress. The structure and functional analysis of GK2848 might provide valuable information on a novel class of carbonic anhydrases, as none of its homologous structures have been characterized

Enrichment of target sequences for next-generation sequencing applications in research and diagnostics.

Science.gov (United States)

Altmüller, Janine; Budde, Birgit S; Nürnberg, Peter

2014-02-01

Abstract Targeted re-sequencing such as gene panel sequencing (GPS) has become very popular in medical genetics, both for research projects and in diagnostic settings. The technical principles of the different enrichment methods have been reviewed several times before; however, new enrichment products are constantly entering the market, and researchers are often puzzled about the requirement to take decisions about long-term commitments, both for the enrichment product and the sequencing technology. This review summarizes important considerations for the experimental design and provides helpful recommendations in choosing the best sequencing strategy for various research projects and diagnostic applications.

Complete genome sequence of Burkholderia sp. strain PAMC28687, a potential octopine-utilizing bacterium isolated from Antarctica lichen.

Science.gov (United States)

Han, So-Ra; Yu, Sang-Cheol; Ahn, Do-Hwan; Park, Hyun; Oh, Tae-Jin

2016-05-20

We report the complete genome sequence of Burkholderia sp. PAMC28687, which was isolated from the Antarctica lichen Useea sp., for better understanding of its catabolic traits in utilizing octopine as a source of carbon/nitrogen between Burkholderia and lichen. The genome consists of three circular chromosomes with five circular plasmids for the total 6,881,273bp sized genome with a G+C content of 58.14%. Copyright © 2016 Elsevier B.V. All rights reserved.

HIV Sequence Compendium 2010

Energy Technology Data Exchange (ETDEWEB)

Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2010-12-31

This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

Effect of fiber angle orientation and stacking sequence on mixed mode fracture toughness of carbon fiber reinforced plastics: Numerical and experimental investigations

International Nuclear Information System (INIS)

Naghipour, P.; Bartsch, M.; Chernova, L.; Hausmann, J.; Voggenreiter, H.

2010-01-01

This paper focuses on the effect of fiber orientation and stacking sequence on the progressive mixed mode delamination failure in composite laminates using fracture experiments and finite element (FE) simulations. Every laminate is modelled numerically combining damageable layers with defined fiber orientations and cohesive zone interface elements, subjected to mixed mode bending. The numerical simulations are then calibrated and validated through experiments, conducted following standardized mixed mode delamination tests. The numerical model is able to successfully capture the experimentally observed effects of fiber angle orientations and variable stacking sequences on the global load-displacement response and mixed mode inter-laminar fracture toughness of the various laminates. For better understanding of the failure mechanism, fracture surfaces of laminates with different stacking sequences are also studied using scanning electron microscopy (SEM).

Almost convergence of triple sequences

OpenAIRE

Ayhan Esi; M.Necdet Catalbas

2013-01-01

In this paper we introduce and study the concepts of almost convergence and almost Cauchy for triple sequences. Weshow that the set of almost convergent triple sequences of 0's and 1's is of the first category and also almost everytriple sequence of 0's and 1's is not almost convergent.Keywords: almost convergence, P-convergent, triple sequence.

Sequence History Update Tool

Science.gov (United States)

Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

2008-01-01

The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

Limits on carbon sequestration in arid blue carbon ecosystems.

Science.gov (United States)

Schile, Lisa M; Kauffman, J Boone; Crooks, Stephen; Fourqurean, James W; Glavan, Jane; Megonigal, J Patrick

2017-04-01

Coastal ecosystems produce and sequester significant amounts of carbon ("blue carbon"), which has been well documented in humid and semi-humid regions of temperate and tropical climates but less so in arid regions where mangroves, marshes, and seagrasses exist near the limit of their tolerance for extreme temperature and salinity. To better understand these unique systems, we measured whole-ecosystem carbon stocks in 58 sites across the United Arab Emirates (UAE) in natural and planted mangroves, salt marshes, seagrass beds, microbial mats, and coastal sabkha (inter- and supratidal unvegetated salt flats). Natural mangroves held significantly more carbon in above- and belowground biomass than other vegetated ecosystems. Planted mangrove carbon stocks increased with age, but there were large differences for sites of similar age. Soil carbon varied widely across sites (2-367 Mg C/ha), with ecosystem averages that ranged from 49 to 156 Mg C/ha. For the first time, microbial mats were documented to contain soil carbon pools comparable to vascular plant-dominated ecosystems, and could arguably be recognized as a unique blue carbon ecosystem. Total ecosystem carbon stocks ranged widely from 2 to 515 Mg C/ha (seagrass bed and mangrove, respectively). Seagrass beds had the lowest carbon stock per unit area, but the largest stock per total area due to their large spatial coverage. Compared to similar ecosystems globally, mangroves and marshes in the UAE have lower plant and soil carbon stocks; however, the difference in soil stocks is far larger than with plant stocks. This incongruent difference between stocks is likely due to poor carbon preservation under conditions of weakly reduced soils (200-350 mV), coarse-grained sediments, and active shoreline migration. This work represents the first attempt to produce a country-wide coastal ecosystem carbon accounting using a uniform sampling protocol, and was motivated by specific policy goals identified by the Abu Dhabi Global

Lower Paleozoic carbonate rocks of Baird Mountains Quadrangle, Alaska

Energy Technology Data Exchange (ETDEWEB)

Dumoulin, J.A.; Harris, A.G.

1985-04-01

Lower Paleozoic carbonate rocks in the Baird Mountains quadrangle form a relatively thin (about 550 m), chiefly shallow-water succession that has been imbricately thrust and metamorphosed to lower greenschist facies. Middle and Upper Cambrian rocks - the first reported from the western Brooks Range - occur in the northeastern quarter of the quadrangle, south of Angayukaqsraq (formerly Hub) Mountain. They consist of marble grading upward into thin-bedded marble/dolostone couplets and contain pelagiellid mollusks, acetretid brachiopods, and agnostid trilobites. Sedimentologic features and the Pelagiellas indicate a shallow-water depositional environment. Overlying these rocks are Lower and Middle Ordovician marble and phyllite containing graptolites and conodonts of midshelf to basinal aspect. Upper Ordovician rocks in this area are bioturbated to laminated dolostone containing warm, shallow-water conodonts. In the Omar and Squirrel Rivers areas to the west, the Lower Ordovician carbonate rocks show striking differences in lithofacies, biofacies, and thickness. Here they are mainly dolostone with locally well-developed fenestral fabric and evaporite molds, and bioturbated to laminated orange- and gray-weathering dolomitic marble. Upper Silurian dolostone, found near Angayukaqsraq Mountain and on the central Squirrel River, contains locally abundant corals and stronmatoporoids. Devonian carbonate rocks are widely distributed in the Baird Mountains quadrangle; at least two distinct sequences have been identified. In the Omar area, Lower and Middle Devonian dolostone and marble are locally cherty and rich in megafossils. In the north-central (Nakolik River) area, Middle and Upper Devonian marble is interlayered with planar to cross-laminated quartz-carbonate metasandstone and phyllite.

Frozen in Time? Microbial strategies for survival and carbon metabolism over geologic time in a Pleistocene permafrost chronosequence

Science.gov (United States)

Mackelprang, R.; Douglas, T. A.; Waldrop, M. P.

2014-12-01

Permafrost soils have received tremendous interest due to their importance as a global carbon store with the potential to be thawed over the coming centuries. Instead of being 'frozen in time,' permafrost contains active microbes. Most metagenomic studies have focused on Holocene aged permafrost. Here, we target Pleistocene aged ice and carbon rich permafrost (Yedoma), which can differ in carbon content and stage of decay. Our aim was to understand how microbes in the permafrost transform organic matter over geologic time and to identify physiological and biochemical adaptations that enable long-term survival. We used next-generation sequencing to characterize microbial communities along a permafrost age gradient. Samples were collected from the Cold Regions Research and Engineering Laboratory (CRREL) Permafrost Tunnel near Fox, AK, which penetrates a hillside providing access to permafrost ranging in age from 12 to 40 kyr. DNA was extracted directly from unthawed samples. 16S rRNA amplicon (16S) and shotgun metagenome sequencing revealed significant age-driven differences. First, microbial diversity declines with permafrost age, likely due to long-term exposure to environmental stresses and a reduction in metabolic resources. Second, we observed taxonomic differences among ages, with an increasing abundance of Firmicutes (endospore-formers) in older samples, suggesting that dormancy is a common survival strategy in older permafrost. Ordination of 16S and metagenome data revealed age-based clustering. Genes differing significantly between age categories included those involved in lipopolysaccharide assembly, cold-response, and carbon processing. These data point to the physiological adaptations to long-term frozen conditions and to the metabolic processes utilized in ancient permafrost. In fact, a gene common in older samples is involved in cadaverine production, which could potentially explain the putrefied smell of Pleistocene aged permafrost. Coupled with soil

Evaluation of Magnetic Resonance Imaging-Compatible Needles and Interactive Sequences for Musculoskeletal Interventions Using an Open High-Field Magnetic Resonance Imaging Scanner

International Nuclear Information System (INIS)

Wonneberger, Uta; Schnackenburg, Bernhard; Streitparth, Florian; Walter, Thula; Rump, Jens; Teichgraeber, Ulf K. M.

2010-01-01

In this article, we study in vitro evaluation of needle artefacts and image quality for musculoskeletal laser-interventions in an open high-field magnetic resonance imaging (MRI) scanner at 1.0T with vertical field orientation. Five commercially available MRI-compatible puncture needles were assessed based on artefact characteristics in a CuSO4 phantom (0.1%) and in human cadaveric lumbar spines. First, six different interventional sequences were evaluated with varying needle orientation to the main magnetic field B0 (0 o to 90 o ) in a sequence test. Artefact width, needle-tip error, and contrast-to-noise ratio (CNR) were calculated. Second, a gradient-echo sequence used for thermometric monitoring was assessed and in varying echo times, artefact width, tip error, and signal-to-noise ratio (SNR) were measured. Artefact width and needle-tip error correlated with needle material, instrument orientation to B0, and sequence type. Fast spin-echo sequences produced the smallest needle artefacts for all needles, except for the carbon fibre needle (width o to B0. Overall, the proton density-weighted spin-echo sequences had the best CNR (CNR Muscle/Needle >16.8). Concerning the thermometric gradient echo sequence, artefacts remained <5 mm, and the SNR reached its maximum at an echo time of 15 ms. If needle materials and sequences are accordingly combined, guidance and monitoring of musculoskeletal laser interventions may be feasible in a vertical magnetic field at 1.0T.

Gymnocypris przewalskii decreases cytosolic carbonic anhydrase expression to compensate for respiratory alkalosis and osmoregulation in the saline-alkaline lake Qinghai.

Science.gov (United States)

Yao, Zongli; Guo, Wenfei; Lai, Qifang; Shi, Jianquan; Zhou, Kai; Qi, Hongfang; Lin, Tingting; Li, Ziniu; Wang, Hui

2016-01-01

Naked carp (Gymnocypris przewalskii), endemic to the saline-alkaline Lake Qinghai, have the capacity to tolerate combined high salinity and alkalinity, but migrate to spawn in freshwater rivers each year. In this study, the full-length cDNA of the cytosolic carbonic anhydrase c isoform of G. przewalskii (GpCAc) was amplified and sequenced; mRNA levels and enzyme activity of GpCAc and blood chemistry were evaluated to understand the compensatory responses as the naked carp returned to the saline-alkaline lake after spawning. We found that GpCAc had a total length of 1400 bp and encodes a peptide of 260 amino acids. Comparison of the deduced amino acid sequences and phylogenetic analysis showed that GpCAc was a member of the cytosolic carbonic anhydrase II-like c family. Cytosolic-carbonic-anhydrase-c-specific primers were used to analyze the tissue distribution of GpCAc mRNA expression. Expression of GpCAc mRNA was found in brain, gill, liver, kidney, gut, and muscle tissues, but primarily in the gill and posterior kidney; however, none was evident in red blood cells. Transferring fish from river water to lake water resulted in a respiratory alkalosis, osmolality, and ion rise in the blood, as well as significant decreases in the expression and enzyme activity of GpCAc in both the gill and kidney within 96 h. These results indicate that GpCAc may play an important role in the acclimation to both high salinity and carbonate alkalinity. Specifically, G. przewalskii decreases cytosolic carbonic anhydrase c expression to compensate for a respiratory alkalosis and to aid in osmoregulation during the transition from river to saline-alkaline lake.

Climate policies between carbon prices, oil rents and urban dynamics

International Nuclear Information System (INIS)

Waisman, H.

2012-01-01

This thesis investigates the effects of constraints imposed on economic interactions by limitations due to natural resources, among which oil and urban land play a crucial role in the context of climate change. These dimensions, often neglected in existing analyses, have an ambiguous effect since they suggest both the risk of enhanced costs if carbon limitations reinforce the sub-optimalities caused by pre-existing constraints, but also, conversely, the possibility of co-benefits if the climate policy helps to correct some pre-existing imperfections of socio-economic trajectories. To investigate this issue, an innovative modeling framework of the energy-economy interactions is elaborated that embarks the specificities of the deployment of oil production capacities and the issues related to the spatial organization in urban areas. We demonstrate that, beyond the carbon price, the costs of climate policy essentially depend on the sequencing of complementary measures, with a crucial role of spatial policy designed to control transport-related emissions through mobility. (author)

SOIL ORGANIC CARBON FRACTIONS AS INFLUENCED BY SOYBEAN CROPPING IN THE HUMID PAMPA OF ARGENTINA

Directory of Open Access Journals (Sweden)

Marta E. Conti

2014-07-01

Full Text Available The sustainability of continuous cropping systems depends heavily on the years of intensive agricultural production and the choice of crop sequence that alters the fractions of soil organic matter. The aim of this study was to evaluate the impact of continuous soybean cultivation on fractions of organic carbon in the vertic Argiudolls of the Argentinean Pampas. Total organic carbon (TOC, particulate organic carbon (POC , fulvic acids (FA, humic acids (HA, humin (H and carbon produced by microbial respiration (Cresp were assessed in plots with continuous production of soybean for over 15 years (SP and grassland plots that were considered the change control (GP. A significant reduction of TOC and POC variables in cultured soybean SP plots, relative to grassland GP, was observed. The POC / TOC and Cresp / TOC ratios were significantly lower in soybean plots than in grasslands used as controls. These ratios were interpreted as a preferential tendency to maintain high rates of mineralization of labile carbon forms and increased biological stability of humified forms in cultured soybean plots. The shapes of the humic fractions of less complexity, FA and HA, were significantly reduced in the latter plots compared with grasslands, while no significant changes occurred in the more stable and recalcitrant forms of carbon, such as humin, in either plot type.

Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

Energy Technology Data Exchange (ETDEWEB)

Storrs, Richard Wood [Univ. of California, Berkeley, CA (United States)

1992-08-01

Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by ³¹P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 Å of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an α-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

Energy Technology Data Exchange (ETDEWEB)

Storrs, R.W.

1992-08-01

Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by [sup 31]P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 [Angstrom] of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an [alpha]-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

Dissolved inorganic carbon and organic carbon in mires in the Forsmark area. A pilot study

Energy Technology Data Exchange (ETDEWEB)

Loefgren, Anders [EcoAnalytica, Haegersten (Sweden)

2011-12-15

Dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) are the large dissolved carbon pools in mires. They are both related to a number of factors such as groundwater flow, minerogenic influence and peat properties, which all are more or less related to peatland development stage. In a scenario of a release of radionuclides from an underground repository containing radioactive material, behaviour of these pools during the mire ontogeny will be of importance for the understanding of how C-14 will constitute a potential risk to humans and non-human biota. In this pilot study, DIC and DOC concentrations were investigated for three mires representing a potential sequence of peatland development in a coastal area at Forsmark in central Sweden characterized by land upheaval, a flat topography and calcareous content in the soil. The mires where chosen based on difference in height above the sea level, covering approximate 1000 years, and characteristics based on their vegetation. Water samples were collected during August from all three mires at two different depths in the anoxic layer of the mires, by extracting water from peat obtained with a peat corer. DIC concentrations where related to the age of the mires, with the lowest concentrations in the highest located mire. There was a positive correlation between pH and DIC, where the higher DIC concentrations were found in the 'richer' fens. DIC concentrations were also positively related to the conductivity within and between the mires, where conductivity would be a proxy for the dominating cation Ca{sup 2+} associated to the calcareous-influenced groundwater. DOC concentrations were highest in the oldest mire, but were similar in the younger mires. No patterns were found between DIC and DOC, and the peat bulk density. The report ends with suggestions on how a continued study could be improved.

Reaction of uranium oxides with chlorine and carbon or carbon monoxide to prepare uranium chlorides

Energy Technology Data Exchange (ETDEWEB)

Haas, P.A.; Lee, D.D.; Mailen, J.C.

1991-11-01

The preferred preparation concept of uranium metal for feed to an AVLIS uranium enrichment process requires preparation of uranium tetrachloride (UCI{sub 4}) by reacting uranium oxides (UO{sub 2}/UO{sub 3}) and chlorine (Cl{sub 2}) in a molten chloride salt medium. UO{sub 2} is a very stable metal oxide; thus, the chemical conversion requires both a chlorinating agent and a reducing agent that gives an oxide product which is much more stable than the corresponding chloride. Experimental studies in a quartz reactor of 4-cm ID have demonstrated the practically of some chemical flow sheets. Experimentation has illustrated a sequence of results concerning the chemical flow sheets. Tests with a graphite block at 850{degrees}C demonstrated rapid reactions of Cl{sub 2} and evolution of carbon dioxide (CO{sub 2}) as a product. Use of carbon monoxide (CO) as the reducing agent also gave rapid reactions of Cl{sub 2} and formation of CO{sub 2} at lower temperatures, but the reduction reactions were slower than the chlorinations. Carbon powder in the molten salt melt gave higher rates of reduction and better steady state utilization of Cl{sub 2}. Addition of UO{sub 2} feed while chlorination was in progress greatly improved the operation by avoiding the plugging effects from high UO{sub 2} concentrations and the poor Cl{sub 2} utilizations from low UO{sub 2} concentrations. An UO{sub 3} feed gave undesirable effects while a feed of UO{sub 2}-C spheres was excellent. The UO{sub 2}-C spheres also gave good rates of reaction as a fixed bed without any molten chloride salt. Results with a larger reactor and a bottom condenser for volatilized uranium show collection of condensed uranium chlorides as a loose powder and chlorine utilizations of 95--98% at high feed rates. 14 refs., 7 figs., 14 tabs.

Dissolved inorganic carbon and organic carbon in mires in the Forsmark area. A pilot study

International Nuclear Information System (INIS)

Loefgren, Anders

2011-12-01

Dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) are the large dissolved carbon pools in mires. They are both related to a number of factors such as groundwater flow, minerogenic influence and peat properties, which all are more or less related to peatland development stage. In a scenario of a release of radionuclides from an underground repository containing radioactive material, behaviour of these pools during the mire ontogeny will be of importance for the understanding of how C-14 will constitute a potential risk to humans and non-human biota. In this pilot study, DIC and DOC concentrations were investigated for three mires representing a potential sequence of peatland development in a coastal area at Forsmark in central Sweden characterized by land upheaval, a flat topography and calcareous content in the soil. The mires where chosen based on difference in height above the sea level, covering approximate 1000 years, and characteristics based on their vegetation. Water samples were collected during August from all three mires at two different depths in the anoxic layer of the mires, by extracting water from peat obtained with a peat corer. DIC concentrations where related to the age of the mires, with the lowest concentrations in the highest located mire. There was a positive correlation between pH and DIC, where the higher DIC concentrations were found in the 'richer' fens. DIC concentrations were also positively related to the conductivity within and between the mires, where conductivity would be a proxy for the dominating cation Ca 2+ associated to the calcareous-influenced groundwater. DOC concentrations were highest in the oldest mire, but were similar in the younger mires. No patterns were found between DIC and DOC, and the peat bulk density. The report ends with suggestions on how a continued study could be improved

GROUPING WEB ACCESS SEQUENCES uSING SEQUENCE ALIGNMENT METHOD

OpenAIRE

BHUPENDRA S CHORDIA; KRISHNAKANT P ADHIYA

2011-01-01

In web usage mining grouping of web access sequences can be used to determine the behavior or intent of a set of users. Grouping websessions is how to measure the similarity between web sessions. There are many shortcomings in traditional measurement methods. The taskof grouping web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-groupsimilarity is done using sequence alignment method. This paper introduces a new method to group we...

Moss and soil contributions to the annual net carbon flux of a maturing boreal forest

Science.gov (United States)

Harden, J.W.; O'Neill, K. P.; Trumbore, S.E.; Veldhuis, H.; Stocks, B.J.

1997-01-01

We used input and decomposition data from 14C studies of soils to determine rates of vertical accumulation of moss combined with carbon storage inventories on a sequence of burns to model how carbon accumulates in soils and moss after a stand-killing fire. We used soil drainage - moss associations and soil drainage maps of the old black spruce (OBS) site at the BOREAS northern study area (NSA) to areally weight the contributions of each moderately well drained, feathermoss areas; poorly drained sphagnum - feathermoss areas; and very poorly drained brown moss areas to the carbon storage and flux at the OBS NSA site. On this very old (117 years) complex of black spruce, sphagnum bog veneer, and fen systems we conclude that these systems are likely sequestering 0.01-0.03 kg C m-2 yr-' at OBS-NSA today. Soil drainage in boreal forests near Thompson, Manitoba, controls carbon storage and flux by controlling moss input and decomposition rates and by controlling through fire the amount and quality of carbon left after burning. On poorly drained soils rich in sphagnum moss, net accumulation and long-term storage of carbon is higher than on better drained soils colonized by feathermosses. The carbon flux of these contrasting ecosystems is best characterized by soil drainage class and stand age, where stands recently burned are net sources of CO2, and maturing stands become increasingly stronger sinks of atmospheric CO2. This approach to measuring carbon storage and flux presents a method of scaling to larger areas using soil drainage, moss cover, and stand age information.

The sequence specificity of UV-induced DNA damage in a systematically altered DNA sequence.

Science.gov (United States)

Khoe, Clairine V; Chung, Long H; Murray, Vincent

2018-06-01

The sequence specificity of UV-induced DNA damage was investigated in a specifically designed DNA plasmid using two procedures: end-labelling and linear amplification. Absorption of UV photons by DNA leads to dimerisation of pyrimidine bases and produces two major photoproducts, cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs). A previous study had determined that two hexanucleotide sequences, 5'-GCTC*AC and 5'-TATT*AA, were high intensity UV-induced DNA damage sites. The UV clone plasmid was constructed by systematically altering each nucleotide of these two hexanucleotide sequences. One of the main goals of this study was to determine the influence of single nucleotide alterations on the intensity of UV-induced DNA damage. The sequence 5'-GCTC*AC was designed to examine the sequence specificity of 6-4PPs and the highest intensity 6-4PP damage sites were found at 5'-GTTC*CC nucleotides. The sequence 5'-TATT*AA was devised to investigate the sequence specificity of CPDs and the highest intensity CPD damage sites were found at 5'-TTTT*CG nucleotides. It was proposed that the tetranucleotide DNA sequence, 5'-YTC*Y (where Y is T or C), was the consensus sequence for the highest intensity UV-induced 6-4PP adduct sites; while it was 5'-YTT*C for the highest intensity UV-induced CPD damage sites. These consensus tetranucleotides are composed entirely of consecutive pyrimidines and must have a DNA conformation that is highly productive for the absorption of UV photons. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.

Azide photochemistry for facile modification of graphitic surfaces: preparation of DNA-coated carbon nanotubes for biosensing

International Nuclear Information System (INIS)

Moghaddam, Minoo J; Yang Wenrong; Bojarski, Barbara; Gengenbach, Thomas R; Gao Mei; Zareie, Hadi; McCall, Maxine J

2012-01-01

A facile, two-step method for chemically attaching single-stranded DNA to graphitic surfaces, represented here by carbon nanotubes, is reported. In the first step, an azide-containing compound, N-5-azido-nitrobenzoyloxy succinimide (ANB-NOS), is used to form photo-adducts on the graphitic surfaces in a solid-state photochemical reaction, resulting in active ester groups being oriented for the subsequent reactions. In the second step, pre-synthesized DNA strands bearing a terminal amine group are coupled in an aqueous solution with the active esters on the photo-adducts. The versatility of the method is demonstrated by attaching pre-synthesized DNA to surfaces of carbon nanotubes in two platforms—as vertically-aligned multi-walled carbon nanotubes on a solid support and as tangled single-walled carbon nanotubes in mats. The reaction products at various stages were characterized by x-ray photoelectron spectroscopy. Two different assays were used to check that the DNA strands attached to the carbon nanotubes were able to bind their partner strands with complementary base sequences. The first assay, using partner DNA strands tethered to gold nanoparticles, enabled the sites of DNA attachment to the carbon nanotubes to be identified in TEM images. The second assay, using radioactively labelled partner DNA strands, quantified the density of functional DNA strands attached to the carbon nanotubes. The diversity of potential applications for these DNA-modified carbon-nanotube platforms is exemplified here by the successful use of a DNA-modified single-walled carbon-nanotube mat as an electrode for the specific detection of metal ions. (paper)

Stable carbon, nitrogen and sulfur isotopes in non-carbonate fractions of cold-seep carbonates

Science.gov (United States)

Feng, Dong; Peng, Yongbo; Peckmann, Jörn; Roberts, Harry; Chen, Duofu

2017-04-01

Sulfate-driven anaerobic oxidation of methane (AOM) supports chemosynthesis-based communities and limits the release of methane from marine sediments. This process promotes the formation of carbonates close to the seafloor along continental margins. The geochemical characteristics of the carbonate minerals of these rocks are increasingly understood, questions remain about the geochemical characteristics of the non-carbonate fractions. Here, we report stable carbon, nitrogen and sulfur isotope patterns in non-carbonate fractions of seep carbonates. The authigenic carbonates were collected from three modern seep provinces (Black Sea, Gulf of Mexico, and South China Sea) and three ancient seep deposits (Marmorito, northern Italy, Miocene; SR4 deposit of the Lincoln Creek Formation and Whiskey Creek, western Washington, USA, Eocene to Oligocene). The δ13C values of non-carbonate fractions range from ˜-25‰ to -80‰ VPDB. These values indicate that fossil methane mixed with varying amounts of pelagic organic matter is the dominant source of carbon in these fractions. The relatively small offset between the δ34S signatures of the non-carbonate fractions and the respective sulfide minerals suggests that locally produced hydrogen sulfide is the main source of sulfur in seep environments. The δ15N values of the non-carbonate fractions are generally lower than the corresponding values of deep-sea sediments, suggesting that organic nitrogen is mostly of a local origin. This study reveals the potential of using δ13C, δ15N, δ34S values to discern seep and non-seep deposits. In cases where δ13Ccarbonate values are only moderately low due to mixing processes and lipid biomarkers have been erased in the course of burial, it is difficult to trace back AOM owing to the lack of other records. This problem is even more pronounced when authigenic carbonate is not available in ancient seep environments. Acknowledgments: The authors thank BOEM and NOAA for their years' support

"First generation" automated DNA sequencing technology.

Science.gov (United States)

Slatko, Barton E; Kieleczawa, Jan; Ju, Jingyue; Gardner, Andrew F; Hendrickson, Cynthia L; Ausubel, Frederick M

2011-10-01

Beginning in the 1980s, automation of DNA sequencing has greatly increased throughput, reduced costs, and enabled large projects to be completed more easily. The development of automation technology paralleled the development of other aspects of DNA sequencing: better enzymes and chemistry, separation and imaging technology, sequencing protocols, robotics, and computational advancements (including base-calling algorithms with quality scores, database developments, and sequence analysis programs). Despite the emergence of high-throughput sequencing platforms, automated Sanger sequencing technology remains useful for many applications. This unit provides background and a description of the "First-Generation" automated DNA sequencing technology. It also includes protocols for using the current Applied Biosystems (ABI) automated DNA sequencing machines. © 2011 by John Wiley & Sons, Inc.

The recurrence sequences via Sylvester matrices

Science.gov (United States)

Karaduman, Erdal; Deveci, Ömür

2017-07-01

In this work, we define the Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by using the Slyvester matrices which are obtained from the characteristic polynomials of the Pell and Jacobsthal sequences and then, we study the sequences defined modulo m. Also, we obtain the cyclic groups and the semigroups from the generating matrices of these sequences when read modulo m and then, we derive the relationships among the orders of the cyclic groups and the periods of the sequences. Furthermore, we redefine Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by means of the elements of the groups and then, we examine them in the finite groups.

Carbon dioxide sequestration by direct mineral carbonation with carbonic acid

Energy Technology Data Exchange (ETDEWEB)

O' Connor, William K.; Dahlin, David C.; Nilsen, David N.; Walters, Richard P.; Turner, Paul C.

2000-01-01

The Albany Research Center (ARC) of the U.S. Dept. of Energy (DOE) has been conducting a series of mineral carbonation tests at its Albany, Oregon, facility over the past 2 years as part of a Mineral Carbonation Study Program within the DOE. Other participants in this Program include the Los Alamos National Laboratory, Arizona State University, Science Applications International Corporation, and the DOE National Energy Technology Laboratory. The ARC tests have focused on ex-situ mineral carbonation in an aqueous system. The process developed at ARC utilizes a slurry of water mixed with a magnesium silicate mineral, olivine [forsterite end member (Mg2SiO4)], or serpentine [Mg3Si2O5(OH)4]. This slurry is reacted with supercritical carbon dioxide (CO2) to produce magnesite (MgCO3). The CO2 is dissolved in water to form carbonic acid (H2CO3), which dissociates to H+ and HCO3 -. The H+ reacts with the mineral, liberating Mg2+ cations which react with the bicarbonate to form the solid carbonate. The process is designed to simulate the natural serpentinization reaction of ultramafic minerals, and for this reason, these results may also be applicable to in-situ geological sequestration regimes. Results of the baseline tests, conducted on ground products of the natural minerals, have been encouraging. Tests conducted at ambient temperature (22 C) and subcritical CO2 pressures (below 73 atm) resulted in very slow conversion to the carbonate. However, when elevated temperatures and pressures are utilized, coupled with continuous stirring of the slurry and gas dispersion within the water column, significant reaction occurs within much shorter reaction times. Extent of reaction, as measured by the stoichiometric conversion of the silicate mineral (olivine) to the carbonate, is roughly 90% within 24 hours, using distilled water, and a reaction temperature of 185?C and a partial pressure of CO2 (PCO2) of 115 atm. Recent tests using a bicarbonate solution, under identical reaction

Carbon dioxide sequestration by direct mineral carbonation with carbonic acid

Energy Technology Data Exchange (ETDEWEB)

O' Connor, W.K.; Dahlin, D.C.; Nilsen, D.N.; Walters, R.P.; Turner, P.C.

2000-07-01

The Albany Research Center (ARC) of the US Department of Energy (DOE) has been conducting a series of mineral carbonation tests at its Albany, Oregon, facility over the past 2 years as part of a Mineral Carbonation Study Program within the DOE. The ARC tests have focused on ex-situ mineral carbonation in an aqueous system. The process developed at ARC utilizes a slurry of water mixed with a magnesium silicate mineral, olivine [forsterite and member (mg{sub 2}SiO{sub 4})], or serpentine [Mg{sub 3}Si{sub 2}O{sub 5}(OH){sub 4}]. This slurry is reacted with supercritical carbon dioxide (CO{sub 2}) to produce magnesite (MgCO{sub 3}). The CO{sub 2} is dissolved in water to form carbonic acid (H{sub 2}CO{sub 3}), which dissociates to H{sup +} and HCO{sub 3}{sup {minus}}. The H{sup +} reacts with the mineral, liberating Mg{sup 2+} cations which react with the bicarbonate to form the solid carbonate. The process is designed to simulate the natural serpentinization reaction of ultramafic minerals, and for this reason, these results may also be applicable to in-situ geological sequestration regimes. Results of the baseline tests, conducted on ground products of the natural minerals, have been encouraging. Tests conducted at ambient temperature (22 C) and subcritical CO{sub 2} pressures (below 73 atm) resulted in very slow conversion to the carbonate. However, when elevated temperatures and pressures are utilized, coupled with continuous stirring of the slurry and gas dispersion within the water column, significant reaction occurs within much shorter reaction times. Extent of reaction, as measured by the stoichiometric conversion of the silicate mineral (olivine) to the carbonate, is roughly 90% within 24 hours, using distilled water, and a reaction temperature of 185 C and a partial pressure of CO{sub 2} (P{sub CO{sub 2}}) of 115 atm. Recent tests using a bicarbonate solution, under identical reaction conditions, have achieved roughly 83% conversion of heat treated serpentine

Carbon fuel cells with carbon corrosion suppression

Science.gov (United States)

Cooper, John F [Oakland, CA

2012-04-10

An electrochemical cell apparatus that can operate as either a fuel cell or a battery includes a cathode compartment, an anode compartment operatively connected to the cathode compartment, and a carbon fuel cell section connected to the anode compartment and the cathode compartment. An effusion plate is operatively positioned adjacent the anode compartment or the cathode compartment. The effusion plate allows passage of carbon dioxide. Carbon dioxide exhaust channels are operatively positioned in the electrochemical cell to direct the carbon dioxide from the electrochemical cell.

Sequence stratigraphy in the middle Ordovician shale successions, mid-east Korea: Stratigraphic variations and preservation potential of organic matter within a sequence stratigraphic framework

Science.gov (United States)

Byun, Uk Hwan; Lee, Hyun Suk; Kwon, Yi Kyun

2018-02-01

The Jigunsan Formation is the middle Ordovician shale-dominated transgressive succession in the Taebaeksan Basin, located in the eastern margin of the North China platform. The total organic carbon (TOC) content and some geochemical properties of the succession exhibit a stratigraphically distinct distribution pattern. The pattern was closely associated with the redox conditions related to decomposition, bulk sedimentation rate (dilution), and productivity. To explain the distinct distribution pattern, this study attempted to construct a high-resolution sequence stratigraphic framework for the Jigunsan Formation. The shale-dominated Jigunsan Formation comprises a lower layer of dark gray shale, deposited during transgression, and an upper layer of greenish gray siltstone, deposited during highstand and falling stage systems tracts. The concept of a back-stepped carbonate platform is adopted to distinguish early and late transgressive systems tracts (early and late TST) in this study, whereas the highstand systems tracts and falling stage systems tracts can be divided by changes in stacking patterns from aggradation to progradation. The late TST would be initiated on a rapidly back-stepping surface of sediments and, just above the surface, exhibits a high peak in TOC content, followed by a gradually upward decrease. This trend of TOC distribution in the late TST continues to the maximum flooding surface (MFS). The perplexing TOC distribution pattern within the late TST most likely resulted from both a gradual reduction in productivity during the late TST and a gradual increase in dilution effect near the MFS interval. The reduced production of organic matter primarily incurred decreasing TOC content toward the MFS when the productivity was mainly governed by benthic biota because planktonic organisms were not widespread in the Ordovician. Results of this study will help improve the understanding of the source rock distribution in mixed carbonate

Carbon isotopic evidence for the associations of decreasing atmospheric CO2 level with the Frasnian-Famennian mass extinction

Science.gov (United States)

Xu, Bing; Gu, Zhaoyan; Wang, Chengyuan; Hao, Qingzhen; Han, Jingtai; Liu, Qiang; Wang, Luo; Lu, Yanwu

2012-03-01

A perturbation of the global carbon cycle has often been used for interpreting the Frasnian-Famennian (F-F) mass extinction. However, the changes of atmospheric CO2 level (pCO2) during this interval are much debatable. To illustrate the carbon cycle during F-F transition, paired inorganic (δ13Ccarb) and organic (δ13Corg) carbon isotope analyses were carried out on two late Devonian carbonate sequences (Dongcun and Yangdi) from south China. The larger amplitude shift of δ13Corg compared to δ13Ccarb and its resultant Δ13C (Δ13C = δ13Ccarb - δ13Corg) decrease indicate decreased atmospheric CO2level around the F-F boundary. The onset ofpCO2 level decrease predates that of marine regressions, which coincide with the beginning of conodont extinctions, suggesting that temperature decrease induced by decreased greenhouse effect of atmospheric CO2might have contributed to the F-F mass extinction.

Swab-to-Sequence: Real-time Data Analysis Platform for the Biomolecule Sequencer

Data.gov (United States)

National Aeronautics and Space Administration — DNA was successfully sequenced on the ISS in 2016, but the DNA sequenced was prepared on the ground. With FY’16 IRAD funds, the same team developed a...

Carbon Fiber Reinforced Carbon Composite Valve for an Internal Combustion Engine

Science.gov (United States)

Rivers, H. Kevin (Inventor); Ransone, Philip O. (Inventor); Northam, G. Burton (Inventor)

1999-01-01

A carbon fiber reinforced carbon composite valve for internal combustion engines and the like formed of continuous carbon fibers throughout the valve's stem and head is disclosed. The valve includes braided carbon fiber material over axially aligned unidirectional carbon fibers forming a valve stem; the braided and unidirectional carbon fibers being broomed out at one end of the valve stem forming the shape of the valve head; the valve-shaped structure being densified and rigidized with a matrix of carbon containing discontinuous carbon fibers: and the finished valve being treated to resist oxidation. Also disclosed is a carbon matrix plug containing continuous and discontinuous carbon fibers and forming a net-shape valve head acting as a mandrel over which the unidirectional and braided carbon fibers are formed according to textile processes. Also disclosed are various preform valves and processes for making finished and preform carbon fiber reinforced carbon composite valves.

Element fractionation by sequential extraction in a soil with high carbonate content

International Nuclear Information System (INIS)

Sulkowski, Margareta; Hirner, Alfred V.

2006-01-01

The influence of carbonate and other buffering substances in soils on the results of a 3-step sequential extraction procedure (BCR) used for metal fractionation was investigated. Deviating from the original extraction scheme, where the extracts are analysed only for a limited number of metals, almost all elements in the soils were quantified by X-ray fluorescence spectroscopy, in the initial samples as well as in the residues of all extraction steps. Additionally, the mineral contents were determined by X-ray diffractometry. Using this methodology, it was possible to correlate changes in soil composition caused by the extraction procedure with the release of elements. Furthermore, the pH values of all extracts were monitored, and certain extraction steps were repeated until no significant pH-rise occurred. A soil with high dolomite content (27%) and a carbonate free soil were extracted. Applying the original BCR-sequence to the calcareous soil, carbonate was found in the residues of the first two steps and extract pH-values rose by around two units in the first and second step, caused mainly by carbonate dissolution. This led to wrong assignment of the carbonate elements Ca, Mg, Sr, Ba, and also to decreased desorption and increased re-adsorption of ions in those steps. After repetition of the acetic acid step until extract pH remained low, the carbonate was completely destroyed and the distributions of the elements Ca, Mg, Sr, Ba as well as those of Co, Ni, Cu, Zn and Pb were found to be quite different to those determined in the original extraction. Furthermore, it could be shown that the effectiveness of the reduction process in step two was reduced by increasing pH: Fe oxides were not significantly attacked by the repeated acetic acid treatments, but a 10-fold amount of Fe was mobilized by hydroxylamine hydrochloride after complete carbonate destruction. On the other hand, only small amounts of Fe were released anyway. Even repeated reduction steps did not

Carbonate-silicate cycle models of the long-term carbon cycle, carbonate accumulation in the oceans, and climate

International Nuclear Information System (INIS)

Caldeira, K.G.

1991-01-01

Several models of the long-term carbon cycle, incorporating models of the carbonate-silicate cycle, were developed and utilized to investigate issues relating to global climate and the causes and consequences of changes in calcium carbonate accumulation in the oceans. Model results indicate that the marked mid-Cretaceous (120 Ma) global warming could be explained by increased rates of release of carbon dioxide from subduction-zone metamorphism and mid-ocean-ridges, in conjunction with paleogeographic factors. Since the mid-Cretaceous, the primary setting for calcium carbonate accumulation in the oceans has shifted from shallow-water to deep-water environments. Model results suggest that this shift could have major consequences for the carbonate-silicate cycle and climate, and lead to significant increases in the flux of metamorphic carbon dioxide to the atmosphere. Increases in pelagic carbonate productivity, and decreases in tropical shallow-water area available for neritic carbonate accumulation, have both been proposed as the primary cause of this shift. Two lines of evidence developed here (one involving a statistical analysis of Tertiary carbonate-accumulation and oxygen-isotope data, and another based on modeling the carbonate-silicate cycle and ocean chemistry) suggest that a decrease in tropical shallow-water area was more important than increased pelagic productivity in explaining this shift. Model investigations of changes in ocean chemistry at the Cretaceous/Tertiary (K/T) boundary (66 Ma) indicate that variations in deep-water carbonate productivity may affect shallow-water carbonate accumulation rates through a mechanism involving surface-water carbonate-ion concentration. In the aftermath of the K/T boundary event, deep-water carbonate production and accumulation were significantly reduced as a result of the extinction of calcareous plankton

Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences.

Science.gov (United States)

Yadav, Shailendra; Kundu, Sharbadeb; Ghosh, Sankar K; Maitra, S S

2015-01-01

Methanogens, a key contributor in global carbon cycling, methane emission, and alternative energy production, generate methane gas via anaerobic digestion of organic matter. The methane emission potential depends upon methanogenic diversity and activity. Since they are anaerobes and difficult to isolate and culture, their diversity present in the landfill sites of Delhi and marshlands of Southern Assam, India, was analyzed using molecular techniques like 16S rDNA sequencing, DGGE, and qPCR. The sequencing results indicated the presence of methanogens belonging to the seventh order and also the order Methanomicrobiales in the Ghazipur and Bhalsawa landfill sites of Delhi. Sequences, related to the phyla Crenarchaeota (thermophilic) and Thaumarchaeota (mesophilic), were detected from marshland sites of Southern Assam, India. Jaccard analysis of DGGE gel using Gel2K showed three main clusters depending on the number and similarity of band patterns. The copy number analysis of hydrogenotrophic methanogens using qPCR indicates higher abundance in landfill sites of Delhi as compared to the marshlands of Southern Assam. The knowledge about "methanogenic archaea composition" and "abundance" in the contrasting ecosystems like "landfill" and "marshland" may reorient our understanding of the Archaea inhabitants. This study could shed light on the relationship between methane-dynamics and the global warming process.

Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences

Directory of Open Access Journals (Sweden)

Shailendra Yadav

2015-01-01

Full Text Available Methanogens, a key contributor in global carbon cycling, methane emission, and alternative energy production, generate methane gas via anaerobic digestion of organic matter. The methane emission potential depends upon methanogenic diversity and activity. Since they are anaerobes and difficult to isolate and culture, their diversity present in the landfill sites of Delhi and marshlands of Southern Assam, India, was analyzed using molecular techniques like 16S rDNA sequencing, DGGE, and qPCR. The sequencing results indicated the presence of methanogens belonging to the seventh order and also the order Methanomicrobiales in the Ghazipur and Bhalsawa landfill sites of Delhi. Sequences, related to the phyla Crenarchaeota (thermophilic and Thaumarchaeota (mesophilic, were detected from marshland sites of Southern Assam, India. Jaccard analysis of DGGE gel using Gel2K showed three main clusters depending on the number and similarity of band patterns. The copy number analysis of hydrogenotrophic methanogens using qPCR indicates higher abundance in landfill sites of Delhi as compared to the marshlands of Southern Assam. The knowledge about “methanogenic archaea composition” and “abundance” in the contrasting ecosystems like “landfill” and “marshland” may reorient our understanding of the Archaea inhabitants. This study could shed light on the relationship between methane-dynamics and the global warming process.

The research of a method for determination of total carbon, combination carbon and free carbon in beryllium metal

International Nuclear Information System (INIS)

Yang Xingzhong; Zhu Xiaohong

1996-02-01

A method for determination of total carbon, combination carbon and free carbon in beryllium metal with LECO CS-344 carbon/sulphur determinant has been studied. Tungsten-copper mixed pellets are used as flux to the determination of total carbon. Ratio of weight of the flux to the sample is greater than 20:1. Good analytical results are got. By this method the relative standard deviation is <10% when the content of total carbon in the range of 0.050%∼0.080% in beryllium. A standard steel sample of carbon is added into beryllium, the recoveries are 94%∼106%. For determination of free carbon, the sample are decomposed with 3 mol/L HCl, filtered and followed determination. By this method the relative standard deviation is ≤10% when the content of free carbon in the range of 0.006%∼0.020% in beryllium. the balance of total carbon and free carbon is equal to combination carbon. The method is used to determine the sample of content of total carbon in the range of 0.050%∼1.00%, free carbon in the range of 0.006%∼0.500% in metal beryllium. (6 refs., 1 fig., 13 tabs.)