Swimming, swarming, twitching, and chemotactic responses of Cupriavidus metallidurans CH34 and Pseudomonas putida mt2 in the presence of cadmium.

PubMed

Shamim, Saba; Rehman, Abdul; Qazi, Mahmood Hussain

2014-04-01

To use of microorganisms for bioremediation purposes, the study of their motility behavior toward metals is essential. In the present study, Cupriavidus metallidurans CH34 and Pseudomonas putida mt2 were used as cadmium (Cd)-resistant and -sensitive bacteria, respectively, to evaluate the effects of Cd on their motility behaviors. Potassium morpholinopropane sulfonate (MOPS) buffer was used to observe the motility behavior of both isolates. Movement of mt2 was less in MOPS buffer compared with CH34, likely reflecting the mono-flagellated nature of mt2 and the peritrichous nature of CH34. The swimming, swarming, twitching, and chemotaxis behaviors of mt2 were greater in the presence of glucose than that of Cd. mt2 exhibited negative motility behaviors when exposed to Cd, but the opposite effect was seen in CH34. Cd was found to be a chemorepellent for mt2 but a chemoattractant for CH34, suggesting that CH34 is a potential candidate for metal (Cd) bioremediation.

ArsR arsenic-resistance regulatory protein from Cupriavidus metallidurans CH34

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

Zhang, Y.; van der Lelie, D.; Monchy, S.

The Cupriavidus metallidurans CH34 arsR gene, which is part of the arsRIC{sub 2}BC{sub 1}HP operon, and its putative arsenic-resistance regulatory protein were identified and characterized. The arsenic-induced transcriptome of C. metallidurans CH34 showed that the genes most upregulated in the presence of arsenate were all located within the ars operon, with none of the other numerous heavy metal resistance systems present in CH34 being induced. A transcriptional fusion between the luxCDABE operon and the arsR promoter/operator (P/O) region was used to confirm the in vivo induction of the ars operon by arsenite and arsenate. The arsR gene was cloned intomore » expression vectors allowing for the overexpression of the ArsR protein as either his-tagged or untagged protein. The ability of the purified ArsR proteins to bind to the ars P/O region was analyzed in vitro by gel mobility shift assays. ArsR showed an affinity almost exclusively to its own ars P/O region. Dissociation of ArsR and its P/O region was metal dependent, and based on decreasing degrees of dissociation three groups of heavy metals could be distinguished: As(III), Bi(III), Co(II), Cu(II), Ni(II); Cd(II); Pb(II) and Zn(II), while no dissociation was observed in the presence of As(V).« less

Toluene degradation by Cupriavidus metallidurans CH34 in nitrate-reducing conditions and in Bioelectrochemical Systems.

PubMed

Tofalos, Anna Espinoza; Daghio, Matteo; González, Myriam; Papacchini, Maddalena; Franzetti, Andrea; Seeger, Michael

2018-05-16

Bioelectrochemical remediation of hydrocarbons is a technology that exploits the ability of specific microorganisms to use as electron acceptor an electrode, thus potentially lowering the operational costs related to classical bioremediation. Several well-characterized hydrocarbonoclastic strains might be electroactive, thus their biodegradation performances in Bioelectrochemical Systems should be studied. Cupriavidus metallidurans CH34 is a model metal-resistant strain whose capacity to degrade benzene aerobically has recently been described. In this study, toluene degradation under anaerobic conditions and the exoelectrogenic capacity of Cupriavidus metallidurans CH34 were determined. Strain CH34 was grown anaerobically with toluene as sole carbon source in sealed serum bottles and then inoculated in a Microbial Electrolysis Cell (MEC) to assess its exoelectrogenic capacity. It was demonstrated for the first time that strain CH34 is able to degrade toluene under nitrate-reducing conditions (up to 45 mgtoluene/L were removed within 17 days, corresponding to 73% of toluene amended). Nitrate consumption and cellular growth were observed during toluene removal. In the MEC, toluene degradation was linked to current production, showing current peaks after every toluene addition (maximum current density 48 mA/m2). Coulombic efficiency of the toluene biodegradation process increased with time, from 11% (first batch cycle), up to 77% (last batch cycle).

Genetic Analysis of Comamonas acidovorans Polyhydroxyalkanoate Synthase and Factors Affecting the Incorporation of 4-Hydroxybutyrate Monomer

PubMed Central

Sudesh, Kumar; Fukui, Toshiaki; Doi, Yoshiharu

1998-01-01

The polyhydroxyalkanoate (PHA) synthase gene of Comamonas acidovorans DS-17 (phaCCa) was cloned by using the synthase gene of Alcaligenes eutrophus as a heterologous hybridization probe. Complete sequencing of a 4.0-kbp SmaI-HindIII (SH40) subfragment revealed the presence of a 1,893-bp PHA synthase coding region which was followed by a 1,182-bp β-ketothiolase gene (phaACa). Both the translated products of these genes showed significant identity, 51.1 and 74.2%, respectively, to the primary structures of the products of the corresponding genes in A. eutrophus. The arrangement of PHA biosynthesis genes in C. acidovorans was also similar to that in A. eutrophus except that the third gene, phaB, coding for acetoacetyl-coenzyme A reductase, was not found in the region downstream of phaACa. The cloned fragment complemented a PHA-negative mutant of A. eutrophus, PHB−4, resulting in poly-3-hydroxybutyrate accumulation of up to 73% of the dry cell weight when fructose was the carbon source. The heterologous expression enabled the incorporation of 4-hydroxybutyrate (4HB) and 3-hydroxyvalerate monomers. The PHA synthase of C. acidovorans does not appear to show any preference for 4-hydroxybutyryl-coenzyme A as a substrate. This leads to the suggestion that in C. acidovorans, it is the metabolic pathway, and not the specificity of the organism’s PHA synthase, that drives the incorporation of 4HB monomers, resulting in the efficient accumulation of PHA with a high 4HB content. PMID:9726894

The stress response of bacterium Cupriavidus metallidurans CH34 into simulated microgravity

NASA Astrophysics Data System (ADS)

van Houdt, Rob; de Boever, Patrick; Coninx, Ilse; Janssen, Ann; Benotmane, Rafi; Leys, Natalie; Mergeay, Max

The stress response of bacterium Cupriavidus metallidurans CH34 into simulated microgravity R. Van Houdt, P. De Boever, I. Coninx, A. Janssen, M.A. Benotmane, N. Leys, and M. Mergeay Expertise group for Molecular and Cellular Biology, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, B-2400 Mol, Belgium. We have studied the response of Cupriavidus (formerly Ralstonia) metallidurans CH34 to simulated microgravity by culturing in a Rotating Wall Vessel (RWV) bioreactor. This bioreactor technology generates a unique Low-Shear Modeled Microgravity (LSMMG) environment and is exploited as analogue for in vivo medical and space environments. Cupriavidus and Ralstonia species are relevant model bacteria since they are often isolated from the floor, air and surfaces of spacecraft assembly rooms and not only contaminate the clean rooms but have also been found prior-to-flight on surfaces of space robots such as the Mars Odyssey Orbiter and even in-flight in ISS cooling water and Shuttle drinking water. In addition, C. metallidurans CH34 is also being used in fundamental space flight experiments aimed to gain a better insight in the bacterial adaptation to space. The first objective was to elucidate the stress response of C. metallidurans CH34 grown in LSMMG compared to a normal gravity control. Transcriptomic analysis revealed that a significant part of the heat shock response was induced in LSMMG. Transcription of d naK, encoding the major heat-shock protein and a prokaryotic homologue of the eukaryotic Hsp70 protein, was induced 6.4 fold in LSMMG. DnaK is assisted by partner chaperones DnaJ and GrpE for which transcription respectively were induced 2.0 and 2.6 fold. Transcription of other chaperones known to belong to the heat shock response was also induced in LSMMG: hslV and hsl U, encoding the HslVU protease, were induced respectively 5.5 and 3.4 fold; htpG, encoding a Hsp90 family chaperone, was induced 4.6 fold

The Effect of Seed Soaking with Rhizobacteria Pseudomonas alcaligenes on the Growth of Swamp Cabbage (Ipomoea reptans Poir)

NASA Astrophysics Data System (ADS)

Widnyana, I. K.; Ngga, M.; Sapanca, P. L. Y.

2018-01-01

The research was conducted to determine the effect of seed soaking with suspense of P. alcaligenes isolate KtSl, TrN2, and TmAl to the growth of swamp cabbage. The research has been initially developed on tomatoes. In this research, Randomized Block Design was chosen as its model while the data analysis was performed by using SPSS v.17 for Windows. Three types of treatment were administered towards P. alcaligenes, namely isolating, soaking, and growing the medium. Some observed parameters were germination and growth. The results showed that seed soaking treatments with suspense P. alcaligenes fostered the germination 25% faster, enhanced the crop up to 24.4%, increased the number of leaves up until 23.15%, lengthen stems to 25%, lengthen the roots up to 46.90%, and increase the fresh weight of stems up until 67.07% and oven-dry weight of stem up to 84.21% compared to the control treatment. The best response of treatment for germination speed was soaking seeds with P. alcaligenes TrN2 for 20 minutes on both NB (Natrium Broth) and PDB (Potato Dextrose Broth) media.

Structure, phase transitions, and isotope effects in [(CH3)4N]2PuCl6

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

Wilson, Richard E.

2015-11-02

The single crystal X-ray diffraction structure of [(CH3)4N]2PuCl6 is presented for the first time, resolving long standing confusion and speculation regarding the structure of this compound in the literature. A temperature dependent study of this compound shows that the structure of [(CH3)4N]2PuCl6 undergoes no fewer than two phase transitions between 100 and 360 K. The phase of [(CH3)4N]2PuCl6 at room temperature is Fd-3c a = 26.012(3) Å. At 360 K, the structure is in space group Fm-3m with a = 13.088(1) Å. The plutonium octahedra and tetramethylammonium cations undergo a rotative displacement and the degree of rotation varies with temperature,more » giving rise to the phase transition from Fm-3m to Fd-3c as the crystal is cooled. Synthesis and structural studies of the deuterated salt [(CD3)4N]2PuCl6 suggest that there is an isotopic effect associated with this phase transition as revealed by a changing transition temperature in the deuterated versus protonated compound indicating that the donor-acceptor interactions between the tetramethylammonium cations and the hexachloroplutonate anions are driving the phase transformation.« less

The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments.

PubMed

Janssen, Paul J; Van Houdt, Rob; Moors, Hugo; Monsieurs, Pieter; Morin, Nicolas; Michaux, Arlette; Benotmane, Mohammed A; Leys, Natalie; Vallaeys, Tatiana; Lapidus, Alla; Monchy, Sébastien; Médigue, Claudine; Taghavi, Safiyh; McCorkle, Sean; Dunn, John; van der Lelie, Daniël; Mergeay, Max

2010-05-05

Many bacteria in the environment have adapted to the presence of toxic heavy metals. Over the last 30 years, this heavy metal tolerance was the subject of extensive research. The bacterium Cupriavidus metallidurans strain CH34, originally isolated by us in 1976 from a metal processing factory, is considered a major model organism in this field because it withstands milli-molar range concentrations of over 20 different heavy metal ions. This tolerance is mostly achieved by rapid ion efflux but also by metal-complexation and -reduction. We present here the full genome sequence of strain CH34 and the manual annotation of all its genes. The genome of C. metallidurans CH34 is composed of two large circular chromosomes CHR1 and CHR2 of, respectively, 3,928,089 bp and 2,580,084 bp, and two megaplasmids pMOL28 and pMOL30 of, respectively, 171,459 bp and 233,720 bp in size. At least 25 loci for heavy-metal resistance (HMR) are distributed over the four replicons. Approximately 67% of the 6,717 coding sequences (CDSs) present in the CH34 genome could be assigned a putative function, and 9.1% (611 genes) appear to be unique to this strain. One out of five proteins is associated with either transport or transcription while the relay of environmental stimuli is governed by more than 600 signal transduction systems. The CH34 genome is most similar to the genomes of other Cupriavidus strains by correspondence between the respective CHR1 replicons but also displays similarity to the genomes of more distantly related species as a result of gene transfer and through the presence of large genomic islands. The presence of at least 57 IS elements and 19 transposons and the ability to take in and express foreign genes indicates a very dynamic and complex genome shaped by evolutionary forces. The genome data show that C. metallidurans CH34 is particularly well equipped to live in extreme conditions and anthropogenic environments that are rich in metals.

The Complete Genome Sequence of Cupriavidus metallidurans Strain CH34, a Master Survivalist in Harsh and Anthropogenic Environments

PubMed Central

Janssen, Paul J.; Van Houdt, Rob; Moors, Hugo; Monsieurs, Pieter; Morin, Nicolas; Michaux, Arlette; Benotmane, Mohammed A.; Leys, Natalie; Vallaeys, Tatiana; Lapidus, Alla; Monchy, Sébastien; Médigue, Claudine; Taghavi, Safiyh; McCorkle, Sean; Dunn, John; van der Lelie, Daniël; Mergeay, Max

2010-01-01

Many bacteria in the environment have adapted to the presence of toxic heavy metals. Over the last 30 years, this heavy metal tolerance was the subject of extensive research. The bacterium Cupriavidus metallidurans strain CH34, originally isolated by us in 1976 from a metal processing factory, is considered a major model organism in this field because it withstands milli-molar range concentrations of over 20 different heavy metal ions. This tolerance is mostly achieved by rapid ion efflux but also by metal-complexation and -reduction. We present here the full genome sequence of strain CH34 and the manual annotation of all its genes. The genome of C. metallidurans CH34 is composed of two large circular chromosomes CHR1 and CHR2 of, respectively, 3,928,089 bp and 2,580,084 bp, and two megaplasmids pMOL28 and pMOL30 of, respectively, 171,459 bp and 233,720 bp in size. At least 25 loci for heavy-metal resistance (HMR) are distributed over the four replicons. Approximately 67% of the 6,717 coding sequences (CDSs) present in the CH34 genome could be assigned a putative function, and 9.1% (611 genes) appear to be unique to this strain. One out of five proteins is associated with either transport or transcription while the relay of environmental stimuli is governed by more than 600 signal transduction systems. The CH34 genome is most similar to the genomes of other Cupriavidus strains by correspondence between the respective CHR1 replicons but also displays similarity to the genomes of more distantly related species as a result of gene transfer and through the presence of large genomic islands. The presence of at least 57 IS elements and 19 transposons and the ability to take in and express foreign genes indicates a very dynamic and complex genome shaped by evolutionary forces. The genome data show that C. metallidurans CH34 is particularly well equipped to live in extreme conditions and anthropogenic environments that are rich in metals. PMID:20463976

Exchange of Xcp (Gsp) secretion machineries between Pseudomonas aeruginosa and Pseudomonas alcaligenes: species specificity unrelated to substrate recognition.

PubMed

de Groot, A; Koster, M; Gérard-Vincent, M; Gerritse, G; Lazdunski, A; Tommassen, J; Filloux, A

2001-02-01

Pseudomonas aeruginosa and Pseudomonas alcaligenes are gram-negative bacteria that secrete proteins using the type II or general secretory pathway, which requires at least 12 xcp gene products (XcpA and XcpP to -Z). Despite strong conservation of this secretion pathway, gram-negative bacteria usually cannot secrete exoproteins from other species. Based on results obtained with Erwinia, it has been proposed that the XcpP and/or XcpQ homologs determine this secretion specificity (M. Linderberg, G. P. Salmond, and A. Collmer, Mol. Microbiol. 20:175-190, 1996). In the present study, we report that XcpP and XcpQ of P. alcaligenes could not substitute for their respective P. aeruginosa counterparts. However, these complementation failures could not be correlated to species-specific recognition of exoproteins, since these bacteria could secrete exoproteins of each other. Moreover, when P. alcaligenes xcpP and xcpQ were expressed simultaneously in a P. aeruginosa xcpPQ deletion mutant, complementation was observed, albeit only on agar plates and not in liquid cultures. After growth in liquid culture the heat-stable P. alcaligenes XcpQ multimers were not detected, whereas monomers were clearly visible. Together, our results indicate that the assembly of a functional Xcp machinery requires species-specific interactions between XcpP and XcpQ and between XcpP or XcpQ and another, as yet uncharacterized component(s).

The interactions of the bacterium Cupriavidus metallidurans CH34 with basalt rock, on Earth and in Space

NASA Astrophysics Data System (ADS)

Byloos, Bo; Van Houdt, Rob; Leys, Natalie; Ilyin, Vyacheslav; Nicholson, Natasha; Childers, Delma; Cockell, Charles; Boon, Nico

2016-07-01

Microbe-mineral interactions have become of interest for space exploration as microorganisms can biomine elements from extra-terrestrial materials, which could be used as nutrients in a life support system. This research is aimed at identifying the molecular mechanisms behind the interaction of Cupriavidus metallidurans CH34 with basalt, a lunar-type rock, and determining the influence of space flight conditions on this interaction. Survival and physiology of CH34 was monitored, with and without basalt, in mineral water over several months by flow cytometry, plate counts, ICP-MS, microscopy and proteomics. To study the influence of space conditions, a flight experiment on board the Russian FOTON-M4 capsule was performed. The results obtained from from water survival experiments on ground showed that CH34 was able to survive in mineral water, in the absence and presence of basalt, for several months. The total cell concentration remained stable but the cultivable fraction dropped to 10%, indicating a transition to a more dormant state. In the presence of basalt, this transition was less pronounced and cultivability was enhanced. In addition, with basalt, CH34 attached to the rock surface and formed a biofilm. The space flight experiment indicated more viable and cultivable cells compared to the ground experiment, both in the absence and presence of basalt, indicating a positive effect of space flight on survival. Chemical analysis indicated that basalt leaches out elements which may contribute to a positive effect of basalt on survival. Basalt may thus enhance survival and viability of CH34 both in ground and space flight experimental conditions. This study hopefully can contribute to a better understanding of microbe-mineral interactions, opening the door to future applications, in space, and on Earth. Acknowledgments: This work is supported by the European Space Agency (ESA-PRODEX) and the Belgian Science Policy (Belspo) through the BIOROCK project. We thank Kai

Hot filament-dissociation of (CH3)3SiH and (CH3)4Si, probed by vacuum ultra violet laser time of flight mass spectroscopy.

PubMed

Sharma, Ramesh C; Koshi, Mitsuo

2006-11-01

The decomposition of trimethylsilane and tetramethylsilane has been investigated for the first time, using hot wire (catalytic) at various temperatures. Trimethylsilane is catalytic-dissociated in these species SiH(2), CH(3)SiH, CH(3), CH(2)Si. Time of flight mass spectroscopy signal of these species are linearly increasing with increasing catalytic-temperature. Time of flight mass spectroscopy (TOFMS) signals of (CH(3))(3)SiH and photodissociated into (CH(3))(2)SiH are decreasing with increasing hot filament temperature. TOFMS signal of (CH(3))(4)Si is decreasing with increasing hot wire temperature, but (CH(3))(3)Si signal is almost constant with increasing the temperature. We calculated activation energies of dissociated species of the parental molecules for fundamental information of reaction kinetics for the first time. Catalytic-dissociation of trimethylsilane, and tetramethylsilane single source time of flight coupled single photon VUV (118 nm) photoionization collisionless radicals at temperature range of tungsten filament 800-2360 K. The study is focused to understand the fundamental information on reaction kinetics of these molecules at hot wire temperature, and processes of catalytic-chemical vapour deposition (Cat-CVD) technique which could be implemented in amorphous and crystalline SiC semiconductors thin films.

Development of eco-friendly bioplastic like PHB by distillery effluent microorganisms.

PubMed

Gangurde, Nilesh S; Sayyed, Riyaz Z; Kiran, Shashi; Gulati, Arvind

2013-01-01

During screening for poly-β-hydroxybutyrate (PHB) producing bacteria from distillery effluent sample, six out of 30 isolates comprising of three strains of Alcaligenes sp., two strains of Bacillus sp., and one strain of Pseudomonas sp. were found to accumulate varying levels of intracellular PHB. Amongst the various isolates, Alcaligenes sp. RZS4 was found as the potent PHB-producing organism, accumulating higher amounts of PHB. PHB productivity was further enhanced in the presence of oxygen, nitrogen-limiting conditions, and cloning of PHB synthesizing genes of Alcaligenes sp. RZS 4 into Escherichia coli. A twofold increase in PHB yield was obtained from recombinant E. coli vis-à-vis Alcaligenes sp.; the recombinant E. coli accumulated more PHB in NDMM, produced good amount of PHB in a single-stage cultivation process under both nutrient-rich and nutrient-deficient conditions. Extraction of PHB with acetone-alcohol (1:1) was found as suitable method for optimum extraction of PHB as this mixture selectively extracted PHB without affecting the non-PHB cell mass. PHB extract from recombinant E. coli showed the presence of C-H, =O stretching, =C-H deformation, =C-H, =CH, and =C-O functional groups characteristic of PHB.

Alcaligenes xylosoxidans endophthalmitis following phacoemulsification and intraocular lens implantation.

PubMed

Robert, Pierre-Yves; Chainier, Delphine; Garnier, Fabien; Ploy, Marie-Cécile; Parneix, Pierre; Adenis, Jean-Paul; Martin, Christian

2008-01-01

Five consecutive cases of endophthalmitis that developed after cataract extraction by a single surgeon using the same operating room during one morning session are described. Following preoperative topical administration of ciprofloxacin, surgery consisted of phacoemulsification with peristaltic pump and fluid venting, polymethylmethacrylate intraocular lens implantation, and corneal suture. No complications occurred during surgery. All five patients developed endophthalmitis caused by infection with Alcaligenes xylosoxidans in less than 24 hours. Pulsed-field gel electrophoresis was used to prove similarity between strains. Bacterial inquiry on contamination of the operating room environment revealed massive colonization of phacoemulsifier irrigation channels by Pseudomonas fluorescens bacteria from an unestablished source. Four of the five patients ultimately recovered visual acuity better than 20/60.

Electrophoretic analysis of cyanide depletion by Pseudomonas alcaligenes.

PubMed

Zaugg, S E; Davidson, R A; Walker, J C; Walker, E B

1997-02-01

Bacterial-facilitated depletion of cyanide is under development for remediation of heap leach operations in the gold mining industry. Capillary electrophoresis was found to be a powerful tool for quantifying cyanide depletion. Changes in cyanide concentration in aqueous suspensions of Pseudomonas alcaligenes bacteria and cyanide at elevated pH were easily monitored by capillary electrophoresis. The resulting data can be used to study rates of cyanide depletion by this strain of bacteria. Concentrations of these bacteria at 10(5) cells/mL were found to reduce cyanide from 100 ppm to less than 8 ppm in four days. In addition, other ions of interest in cyanide metabolism, such as formate, can be simultaneously analyzed. Direct UV detection of cyanide at 192 nm further simplifies the analytical method for these ions.

Molecular weight-dependent degradation of D-lactate-containing polyesters by polyhydroxyalkanoate depolymerases from Variovorax sp. C34 and Alcaligenes faecalis T1.

PubMed

Sun, Jian; Matsumoto, Ken'ichiro; Tabata, Yuta; Kadoya, Ryosuke; Ooi, Toshihiko; Abe, Hideki; Taguchi, Seiichi

2015-11-01

Polyhydroxyalkanoate depolymerase derived from Variovorax sp. C34 (PhaZVs) was identified as the first enzyme that is capable of degrading isotactic P[67 mol% (R)-lactate(LA)-co-(R)-3-hydroxybutyrate(3HB)] [P(D-LA-co-D-3HB)]. This study aimed at analyzing the monomer sequence specificity of PhaZVs for hydrolyzing P(LA-co-3HB) in comparison with a P(3HB) depolymerase from Alcaligenes faecalis T1 (PhaZAf) that did not degrade the same copolymer. Degradation of P(LA-co-3HB) by action of PhaZVs generated dimers, 3HB-3HB, 3HB-LA, LA-3HB, and LA-LA, and the monomers, suggesting that PhaZVs cleaved the linkages between LA and 3HB units and between LA units. To provide a direct evidence for the hydrolysis of these sequences, the synthetic methyl trimers, 3HB-3HB-3HB, LA-LA-3HB, LA-3HB-LA, and 3HB-LA-LA, were treated with the PhaZs. Unexpectedly, not only PhaZVs but also PhaZAf hydrolyzed all of these substrates, namely PhaZAf also cleaved LA-LA linkage. Considering the fact that both PhaZs did not degrade P[(R)-LA] (PDLA) homopolymer, the cleavage capability of LA-LA linkage by PhaZs was supposed to depend on the length of the LA-clustering region in the polymer chain. To test this hypothesis, PDLA oligomers (6 to 40 mer) were subjected to the PhaZ assay, revealing that there was an inverse relationship between molecular weight of the substrates and their hydrolysis efficiency. Moreover, PhaZVs exhibited the degrading activity toward significantly longer PDLA oligomers compared to PhaZAf. Therefore, the cleaving capability of PhaZs used here toward the D-LA-based polymers containing the LA-clustering region was strongly associated with the substrate length, rather than the monomer sequence specificity of the enzyme.

Electron-Rich Carboranes. Studies of a Stereochemically Novel System, (CH3)4C4B7H9, and 11-Vertex Arachno Cluster.

DTIC Science & Technology

1981-01-01

FINSTER , R N GRIMES NOGOIR-75C-0305 UNCLASSIFIED TR-37 NL EOMEEEhE OFFICE OF NAVAL RESEARCH CONTRACT NO. i14.-7-C-31 q,4 TECHNICAL REPORT NO. 37L&#34 0...Electron-Rich Carboranes. Studies of a Stereochemically Novel System, (CH&#34) 4C4 BH 9 , an 11-Vertex Arachno Cluster. .) David C./ Finster aad Russell N...System, (CH3 )4C4B7H9 , an l-Vertex Arachno Cluster 1 David C. Finster and Russell N. Grimes* Contribution from the Department of Chemistry University of

Bioaugmented sulfur-oxidizing denitrification system with Alcaligenes defragrans B21 for high nitrate containing wastewater treatment.

PubMed

Flores, Angel; Nisola, Grace M; Cho, Eulsaeng; Gwon, Eun-Mi; Kim, Hern; Lee, Changhee; Park, Shinjung; Chung, Wook-Jin

2007-05-01

The performance of enriched sludge augmented with the B21 strain of Alcaligenes defragrans was compared with that of enriched sludge, as well as with pure Alcaligenes defragrans B21, in the context of a sulfur-oxidizing denitrification (SOD) process. In synthetic wastewater treatment containing 100-1,000 mg NO3-N/L, the single strain-seeded system exhibited superior performance, featuring higher efficiency and a shorter startup period, provided nitrate loading rate was less than 0.2 kg NO3-N/m(3) per day. At nitrate loading rate of more than 0.5 kg NO3-N/m(3) per day, the bioaugmented sludge system showed higher resistance to shock loading than two other systems. However, no advantage of the bioaugmented system over the enriched sludge system without B21 strain was observed in overall efficiency of denitrification. Both the bioaugmented sludge and enriched sludge systems obtained stable denitrification performance of more than 80% at nitrate loading rate of up to 2 kg NO3-N/m(3) per day.

Characterization of diverse 2,4-dichlorophenoxyacetic acid-degradative plasmids isolated from soil by complementation.

PubMed Central

Top, E M; Holben, W E; Forney, L J

1995-01-01

The diversity of 2,4-dichlorophenoxyacetic acid (2,4-D)-degradative plasmids in the microbial community of an agricultural soil was examined by complementation. This technique involved mixing a suitable Alcaligenes eutrophus (Rifr) recipient strain with the indigenous microbial populations extracted from soil. After incubation of this mixture, Rifr recipient strains which grow with 2,4-D as the only C source were selected. Two A. eutrophus strains were used as recipients: JMP228 (2,4-D-), which was previously derived from A. eutrophus JMP134 by curing of the 2,4-D-degradative plasmid pJP4, and JMP228 carrying pBH501aE (a plasmid derived from pJP4 by deletion of a large part of the tfdA gene which encodes the first step in the mineralization of 2,4-D). By using agricultural soil that had been treated with 2,4-D for several years, transconjugants were obtained with both recipients. However, when untreated control soil was used, no transconjugants were isolated. The various transconjugants had plasmids with seven different EcoRI restriction patterns. The corresponding plasmids are designated pEMT1 to pEMT7. Unlike pJP4, pEMT1 appeared not to be an IncP1 plasmid, but all the others (pEMT2 to pEMT7) belong to the IncP1 group. Hybridization with individual probes for the tfdA to tfdF genes of pJP4 demonstrated that all plasmids showed high degrees of homology to the tfdA gene. Only pEMT1 showed a high degree of homology to tfdB, tfdC, tfdD, tfdE, and tfdF, while the others showed only moderate degrees of homology to tfdB and low degrees of homology to tfdC.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7646006

Genomic Characterization of VIM Metallo-β-Lactamase-Producing Alcaligenes faecalis from Gaza, Palestine.

PubMed

Al Laham, Nahed; Chavda, Kalyan D; Cienfuegos-Gallet, Astrid V; Kreiswirth, Barry N; Chen, Liang

2017-11-01

Carbapenemase-producing Gram-negative bacteria (CP-GNB) have increasingly spread worldwide, and different families of carbapenemases have been identified in various bacterial species. Here, we report the identification of five VIM metallo-β-lactamase-producing Alcaligenes faecalis isolates associated with a small outbreak in a large hospital in Gaza, Palestine. Next-generation sequencing analysis showed bla VIM-2 is harbored by a chromosomal genomic island among three strains, while bla VIM-4 is carried by a novel plasmid in two strains. Copyright © 2017 American Society for Microbiology.

Modeling solubility and acid-base properties of some amino acids in aqueous NaCl and (CH3)4NCl aqueous solutions at different ionic strengths and temperatures.

PubMed

Bretti, Clemente; Giuffrè, Ottavia; Lando, Gabriele; Sammartano, Silvio

2016-01-01

New potentiometric experiments have been performed in NaCl and in (CH3)4NCl media, to determine the protonation constants, the protonation enthalpy changes and the solubility of six natural α-amino acids, namely Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Serine (Ser) and Phenylalanine (Phe). The aim of the work is the rationalization of the protonation thermodynamics (log [Formula: see text], solubility and [Formula: see text]) in NaCl, determining recommended, tentative or provisional values in selected experimental conditions and to report, for the first time, data in a weak interacting medium, as (CH3)4NCl. Literature data analysis was performed selecting the most reliable values, analyzed together with new data here reported. Significant trends and similarities were observed in the behavior of the six amino acids, and in some cases it was possible to determine common parameters for the ionic strength and temperature dependence. In general, the first protonation step, relative to the amino group, is significantly exothermic (average value is [Formula: see text] = -44.5 ± 0.4 kJ mol(-1) at infinite dilution and T = 298.15 K), and the second, relative to the carboxylate group, is fairly close to zero ([Formula: see text] = -2.5 ± 1.6, same conditions). In both cases, the main contribution to the proton binding reaction is mainly entropic in nature. For phenylalanine and leucine, solubility measurements at different concentrations of supporting electrolyte allowed to determine total and specific solubility values, then used to obtain the Setschenow and the activity coefficients of all the species involved in the protonation equilibria. The values of the first protonation constant in (CH3)4NCl are lower than the corresponding values in NaCl, due to the weak interaction between the deprotonated amino group and (CH3)4N(+). In this light, differences between the protonation functions in NaCl and (CH3)4NCl were used for the quantification

Strain of alcaligenes latus bacteria used for the decomposition of polychlorinated biphenyls

DOEpatents

Dyadischev, Nikolai Romanovich; Zharikov, Gennady Alekseevich; Kapranov, Vladimir Vladimirovich

2001-09-11

Alcaligenes latus bacterial strain TXD-13 VKPM B 75-05 is capable of degrading polychlorinated biphenyls (PCBs). The strain may be employed to detoxicate environment media and PCB-containing industrial waste. To produce biomass, the strain is incubated on media which contain carbon sources, nitrogen sources and mineral salts. The strain is cultivated by a subsurface method up to a titer from 6.0.multidot.10.sup.8 to 2.0.times.10.sup.9 cells per cu cm. The produced biomass is used for degrading PCBs in concentrations from 10.sup.7 to 10.sup.8 cells per cu cm. The strain ensures from 35 to 50% reduction in PCB content in soil and water.

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2007-08-15

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2007-06-15

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2007-09-20

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2006-06-20

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2006-01-18

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2006-08-15

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2006-12-20

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2007-02-15

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2006-09-15

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

Capture of a catabolic plasmid that encodes only 2,4-dichlorophenoxyacetic acid:alpha-ketoglutaric acid dioxygenase (TfdA) by genetic complementation.

PubMed Central

Top, E M; Maltseva, O V; Forney, L J

1996-01-01

The modular pathway for the metabolism of 2,4-dichlorophenoxyacetic acid (2,4-D) encoded on plasmid pJP4 of Alcaligenes eutrophus JMP134 appears to be an example in which two genes, tfdA and tfdB, have been recruited during the evolution of a catabolic pathway. The products of these genes act to convert 2,4-D to a chloro-substituted catechol that can be further metabolized by enzymes of a modified ortho-cleavage pathway encoded by tfdCDEF. Given that modified ortho-cleavage pathways are comparatively common and widely distributed among bacteria, we sought to determine if microbial populations in soil carry tfdA on plasmid vectors that lack tfdCDEF or tfdB. To capture such plasmids from soil populations, we used a recipient strain of A. eutrophus that was rifampin resistant and carried a derivative of plasmid pJP4 (called pBH501aE) in which the tfdA had been deleted. Upon mating with mixed bacterial populations from soil treated with 2,4-D, transconjugants that were resistant to rifampin yet able to grow on 2,4-D were obtained. Among the transconjugants obtained were clones that contained a ca. 75-kb plasmid, pEMT8. Bacterial hosts that carried this plasmid in addition to pBH501aE metabolized 2,4-D, whereas strains with only pEMT8 did not. Southern hybridization showed that pEMT8 encoded a gene with a low level of similarity to the tfdA gene from plasmid pJP4. Using oligonucleotide primers based on known tfdA sequences, we amplified a 330-bp fragment of the gene and determined that it was 77% similar to the tfdA gene of plasmid pJP4 and 94% similar to tfdA from Burkholderia sp. strain RASC. Plasmid pEMT8 lacked genes that exhibited significant levels of homology to tfdB and tfdCDEF. Moreover, cell extracts from A. eutrophus(pEMT8) cultures did not exhibit TfdB, TfdC, TfdD, and TfdE activities, whereas cell extracts from A. eutrophus(pEMT8)(pBH501aE) cultures did. These data suggest that pEMT8 encodes only tfdA and that this gene can effectively complement the tfd

Effect of nitrogen source on curdlan production by Alcaligenes faecalis ATCC 31749.

PubMed

Jiang, Longfa

2013-01-01

This study aims to investigate the effect of nitrogen source on curdlan production by Alcaligenes faecalis ATCC 31749. Curdlan production fell when excess nitrogen source was present, while biomass accumulation increased as the level of nitrogen source raised. Curdlan production and biomass accumulation were greater with urea compared with those with other nitrogen sources. The highest production of curdlan and biomass accumulation by A. faecalis ATCC 31749 was 28.16 g L(-1) and 9.58 g L(-1), respectively, with urea, whereas those with NH(4)Cl were 15.17 g L(-1) and 6.25 g L(-1), respectively. The optimum fermentation time for curdlan production was also affected by the nitrogen source in the medium. Copyright © 2012 Elsevier B.V. All rights reserved.

Interactions between Pteris vittata L. genotypes and a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium (Alcaligenes sp.) in arsenic uptake and PAH-dissipation.

PubMed

Sun, Lu; Zhu, Ganghui; Liao, Xiaoyong; Yan, Xiulan

2017-11-01

The effects of two Pteris vittata L. accessions and a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium (Alcaligenes sp.) on arsenic (As) uptake and phenanthrene dissipation were studied. The Alcaligenes sp. survived in the rhizosphere and improved soil As bioavailability with co-exposure. However, bacterial inoculation altered Pteris vittata L. stress tolerance, and substantially affected the As distribution in the rhizosphere of the two P. vittata accessions. Bacterial inoculation was beneficial to protect the Guangxi accession against the toxic effects, and significantly increased plant As and phenanthrene removal ratios by 27.8% and 2.89%, respectively. In contrast, As removal was reduced by 29.8% in the Hunan accession, when compared with corresponding non-inoculated treatments. We conclude that plant genotype selection is critically important for successful microorganism-assisted phytoremediation of soil co-contaminated with As and PAHs, and appropriate genotype selection may enhance remediation efficiency. Copyright © 2017 Elsevier Ltd. All rights reserved.

Metal induced changes in trivalent chromium resistant Alcaligenes faecalis VITSIM2.

PubMed

Matilda, Shiny C; Shanthi, Chittibabu

2017-05-01

The changes induced in bacterial strains under stress conditions provide an insight into metal resistance strategies. Trivalent chromium resistant bacterium were isolated and identified by 16S rRNA gene sequencing and designated as Alcaligenes faecalis VITSIM2. The growth pattern was monitored. The organism also showed resistance to copper, cadmium, and certain antibiotics. The differentially expressed proteins in SDS PAGE were identified by mass spectrometry as flagellin and 50S ribosomal L36 protein. The morphological changes were identified by scanning electron microscopy. The changes in the cell wall content were estimated by peptidoglycan analysis and transformation of phosphates was detected by 31 P NMR. Flow cytometry was employed to measure the membrane integrity, esterase activity and intracellular pH. In conclusion spectrum of proteomic, physiological, and morphological alterations was observed that aid the organism to overcome chromium stress. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Uncovering the CH-53E Doppler Myth

DTIC Science & Technology

2008-01-01

The Corps’ Changing Super Stallion 8 Helicopter Night Vision System 9 Heads-Up Display (BUD) 9 The Infamous Doppler 12 )FUTURE SOLUTIONS 14 Universal...ABSTRACTION FROM, OR REPRODUCTION OF ALL OR ANY PART OF THIS DOCUMENT IS PERMITTED PROVIDED PROPER ACKNOWLEDGEMENT IT MADE. List ofIllustrations Page...remains intimately familiar to those flying the Marine Corps’ CH-53E &#34Super Stallion &#34 today. Fortunately, the CH.-53Es flown throughout the world today

Identification of the region of a 14-kilodalton protein of Rhodococcus ruber that is responsible for the binding of this phasin to polyhydroxyalkanoic acid granules.

PubMed Central

Pieper-Fürst, U; Madkour, M H; Mayer, F; Steinbüchel, A

1995-01-01

The function of the polyhydroxyalkanoic acid (PHA) granule-associated GA14 protein of Rhodococcus ruber was investigated in Escherichia coli XL1-Blue, which coexpressed this protein with the polyhydroxybutyric acid (PHB) biosynthesis operon of Alcaligenes eutrophus. The GA14 protein had no influence on the biosynthesis rate of PHB in E. coli XL1-Blue(pSKCO7), but this recombinant E. coli strain formed smaller PHB granules than were formed by an E. coli strain that expressed only the PHB operon. Immunoelectron microscopy with GA14-specific antibodies demonstrated the binding of GA14 protein to these mini granules. In a previous study, two hydrophobic domains close to the C terminus of the GA14 protein were analyzed, and a working hypothesis that suggested an anchoring of the GA14 protein in the phospholipid monolayer surrounding the PHA granule core by these hydrophobic domains was developed (U. Pieper-Fürst, M. H. Madkour, F. Mayer, and A. Steinbüchel, J. Bacteriol. 176:4328-4337, 1994). This hypothesis was confirmed by the construction of C-terminally truncated variants of the GA14 protein lacking the second or both hydrophobic domains and by the demonstration of their inability to bind to PHB granules. Further confirmation of the hypothesis was obtained by the construction of a fusion protein composed of the acetaldehyde dehydrogenase II of A. eutrophus and the C terminus of the GA14 protein containing both hydrophobic domains and by its affinity to native and artificial PHB granules. PMID:7730285

On the formation of the ·CH 2CH 2CH=NH 2+ distonic radical cation upon ionization of cyclopropylamine and allylamine

NASA Astrophysics Data System (ADS)

Nguyen, Minh Tho; Creve, Steven; Ha, Tae-Kyu

1998-08-01

Ab initio molecular orbital and density functional theory calculations have been applied to determine the relative stability of the cyclopropylamine 1 and allylamine (CH 2=CHCH 2NH 2+·2) radical cations and their isomers. It is confirmed that, upon ionization, 1 undergoes barrier-free ring-opening giving the distonic species ·CH 2CH 2CH=NH 2+3. 2 also rearranges by a 1,2-H-shift to the more stable 3 (by 70 kJ/mol) which is, however, less stable than the 1-aminopropene ion (CH 3-CH=CH-NH 2+·4) by 60 kJ/mol. The transition structure TS 2/3 lies 40 kJ/mol higher in energy than TS 3/4. Although QCISD and B3LYP calculations of isotropic hyperfine coupling constants agree reasonably with observed values, supporting the presence of the distonic 3 in ESR matrix experiments, the exclusive observation of 3, but not 4, is intriguing. This emphasizes the role of the matrix in stabilizing 3.

Mathematical model for determining the effects of intracytoplasmic inclusions on volume and density of microorganisms.

PubMed Central

Mas, J; Pedrós-Alió, C; Guerrero, R

1985-01-01

Procaryotic microorganisms accumulate several polymers in the form of intracellular inclusions as a strategy to increase survival in a changing environment. Such inclusions avoid osmotic pressure increases by tightly packaging certain macromolecules into the inclusion. In the present paper, a model describing changes in volume and density of the microbial cell as a function of the weight of the macromolecule forming the inclusion is derived from simple theoretical principles. The model is then tested by linear regression with experimental data from glycogen accumulation in Escherichia coli, poly-beta-hydroxybutyrate accumulation in Alcaligenes eutrophus, and sulfur accumulation in Chromatium spp. The model predicts a certain degree of hydration of the polymer in the inclusion and explains both the linear relationship between volume of the cell and weight of the polymer and the hyperbolic relationship between density of the cell and weight of the polymer. Other implications of the model are also discussed. PMID:3902798

Synthetic phytochelatin surface display in Cupriavidus metallidurans CH34 for enhanced metals bioremediation.

PubMed

Biondo, Ronaldo; da Silva, Felipe Almeida; Vicente, Elisabete José; Souza Sarkis, Jorge Eduardo; Schenberg, Ana Clara Guerrini

2012-08-07

This work describes the effects of the cell surface display of a synthetic phytochelatin in the highly metal tolerant bacterium Cupriavidus metallidurans CH34. The EC20sp synthetic phytochelatin gene was fused between the coding sequences of the signal peptide (SS) and of the autotransporter β-domain of the Neisseria gonorrhoeae IgA protease precursor (IgAβ), which successfully targeted the hybrid protein toward the C. metallidurans outer membrane. The expression of the SS-EC20sp-IgAβ gene fusion was driven by a modified version of the Bacillus subtilis mrgA promoter showing high level basal gene expression that is further enhanced by metal presence in C. metallidurans. The recombinant strain showed increased ability to immobilize Pb(2+), Zn(2+), Cu(2+), Cd(2+), Mn(2+), and Ni(2+) ions from the external medium when compared to the control strain. To ensure plasmid stability and biological containment, the MOB region of the plasmid was replaced by the E. coli hok/sok coding sequence.

Separation and characterization of effective demulsifying substances from surface of Alcaligenes sp. S-XJ-1 and its application in water-in-kerosene emulsion.

PubMed

Huang, Xiangfeng; Peng, Kaiming; Feng, Yi; Liu, Jia; Lu, Lijun

2013-07-01

The main goal of this work was to analyze the effect of surface substances on demulsifying capability of the demulsifying strain Alcaligenes sp. S-XJ-1. The demulsifying substances were successfully separated from the cell surface with dichloromethane-alkali treatment, and exhibited 67.5% of the demulsification ratio for water-in-kerosene emulsions at a dosage of 356mg/L. FT-IR, TLC and ESI-MS analysis confirmed the presence of a carbohydrate-protein-lipid complex in the demulsifying substances with the major molecular ions from mass-to-charge ratio (m/z) 165 to 814. After the substances separated, the cell morphology changed from aggregated to dispersed, and the concentration of cell surface functional groups decreased. Cell surface hydrophobicity and the ability of cell adhesion to hydrophobic surface of the treated cells was also reduced compared with original cell. It was proved that the demulsifying substances had a significant effect on cell surface properties and accordingly with demulsifying capability of Alcaligenes sp. S-XJ-1. Copyright © 2013 Elsevier Ltd. All rights reserved.

Uranium Interaction with Two Multi-Resistant Environmental Bacteria: Cupriavidus metallidurans CH34 and Rhodopseudomonas palustris

PubMed Central

Llorens, Isabelle; Untereiner, Guillaume; Jaillard, Danielle; Gouget, Barbara; Chapon, Virginie; Carriere, Marie

2012-01-01

Depending on speciation, U environmental contamination may be spread through the environment or inversely restrained to a limited area. Induction of U precipitation via biogenic or non-biogenic processes would reduce the dissemination of U contamination. To this aim U oxidation/reduction processes triggered by bacteria are presently intensively studied. Using X-ray absorption analysis, we describe in the present article the ability of Cupriavidus metallidurans CH34 and Rhodopseudomonas palustris, highly resistant to a variety of metals and metalloids or to organic pollutants, to withstand high concentrations of U and to immobilize it either through biosorption or through reduction to non-uraninite U(IV)-phosphate or U(IV)-carboxylate compounds. These bacterial strains are thus good candidates for U bioremediation strategies, particularly in the context of multi-pollutant or mixed-waste contaminations. PMID:23251623

Methanesulfonates of high-valent metals: syntheses and structural features of MoO2(CH3SO3)2, UO2(CH3SO3)2, ReO3(CH3SO3), VO(CH3SO3)2, and V2O3(CH3SO3)4 and their thermal decomposition under N2 and O2 atmosphere.

PubMed

Betke, Ulf; Neuschulz, Kai; Wickleder, Mathias S

2011-11-04

Oxide methanesulfonates of Mo, U, Re, and V have been prepared by reaction of MoO(3), UO(2)(CH(3)COO)(2)·2H(2)O, Re(2)O(7)(H(2)O)(2), and V(2)O(5) with CH(3)SO(3)H or mixtures thereof with its anhydride. These compounds are the first examples of solvent-free oxide methanesulfonates of these elements. MoO(2)(CH(3)SO(3))(2) (Pbca, a=1487.05(4), b=752.55(2), c=1549.61(5) pm, V=1.73414(9) nm(3), Z=8) contains [MoO(2)] moieties connected by [CH(3)SO(3)] ions to form layers parallel to (100). UO(2)(CH(3)SO(3))(2) (P2(1)/c, a=1320.4(1), b=1014.41(6), c=1533.7(1) pm, β=112.80(1)°, V=1.8937(3) nm(3), Z=8) consists of linear UO(2)(2+) ions coordinated by five [CH(3)SO(3)] ions, forming a layer structure. VO(CH(3)SO(3))(2) (P2(1)/c, a=1136.5(1), b=869.87(7), c=915.5(1) pm, β=113.66(1)°, V=0.8290(2) nm(3), Z=4) contains [VO] units connected by methanesulfonate anions to form corrugated layers parallel to (100). In ReO(3)(CH(3)SO(3)) (P1, a=574.0(1), b=1279.6(3), c=1641.9(3) pm, α=102.08(2), β=96.11(2), γ=99.04(2)°, V=1.1523(4) nm(3), Z=8) a chain structure exhibiting infinite O-[ReO(2)]-O-[ReO(2)]-O chains is formed. Each [ReO(2)]-O-[ReO(2)] unit is coordinated by two bidentate [CH(3)SO(3)] ions. V(2)O(3)(CH(3)SO(3))(4) (I2/a, a=1645.2(3), b=583.1(1), c=1670.2(3) pm, β=102.58(3), V=1.5637(5) pm(3), Z=4) adopts a chain structure, too, but contains discrete [VO]-O-[VO] moieties, each coordinated by two bidentate [CH(3)SO(3)] ligands. Additional methanesulfonate ions connect the [V(2)O(3)] groups along [001]. Thermal decomposition of the compounds was monitored under N(2) and O(2) atmosphere by thermogravimetric/differential thermal analysis and XRD measurements. Under N(2) the decomposition proceeds with reduction of the metal leading to the oxides MoO(2), U(3)O(7), V(4)O(7), and VO(2); for MoO(2)(CH(3)SO(3))(2), a small amount of MoS(2) is formed. If the thermal decomposition is carried out in a atmosphere of O(2) the oxides MoO(3) and V(2)O(5) are formed. Copyright �

Rhizosphere colonization and arsenic translocation in sunflower (Helianthus annuus L.) by arsenate reducing Alcaligenes sp. strain Dhal-L.

PubMed

Cavalca, Lucia; Corsini, Anna; Bachate, Sachin Prabhakar; Andreoni, Vincenza

2013-10-01

In the present study, six arsenic-resistant strains previously isolated were tested for their plant growth promoting characteristics and heavy metal resistance, in order to choose one model strain as an inoculum for sunflower plants in pot experiments. The aim was to investigate the effect of arsenic-resistant strain on sunflower growth and on arsenic uptake from arsenic contaminated soil. Based on plant growth promoting characteristics and heavy metal resistance, Alcaligenes sp. strain Dhal-L was chosen as an inoculum. Beside the ability to reduce arsenate to arsenite via an Ars operon, the strain exhibited 1-amino-cyclopropane-1-carboxylic acid deaminase activity and it was also able to produce siderophore and indole acetic acid. Pot experiments were conducted with an agricultural soil contaminated with arsenic (214 mg kg⁻¹). A real time PCR method was set up based on the quantification of ACR3(2) type of arsenite efflux pump carried by Alcaligenes sp. strain Dhal-L, in order to monitor presence and colonisation of the strain in the bulk and rhizospheric soil. As a result of strain inoculation, arsenic uptake by plants was increased by 53 %, whereas ACR3(2) gene copy number in rhizospheric soil was 100 times higher in inoculated than in control pots, indicating the colonisation of strain. The results indicated that the presence of arsenate reducing strains in the rhizosphere of sunflower influences arsenic mobilization and promotes arsenic uptake by plant.

40 CFR 1065.660 - THC, NMHC, and CH4 determination.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 34 2012-07-01 2012-07-01 false THC, NMHC, and CH4 determination. 1065... POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calculations and Data Requirements § 1065.660 THC, NMHC, and CH4 determination. (a) THC determination and initial THC/CH 4 contamination corrections. (1) If we...

40 CFR 1065.660 - THC, NMHC, and CH4 determination.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 34 2013-07-01 2013-07-01 false THC, NMHC, and CH4 determination. 1065... POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calculations and Data Requirements § 1065.660 THC, NMHC, and CH4 determination. (a) THC determination and initial THC/CH 4 contamination corrections. (1) If we...

Chemical Forms of Selenium in the Metal-Resistant Bacterium Ralstonia metallidurans CH34 Exposed to Selenite and Selenate

PubMed Central

Sarret, Géraldine; Avoscan, Laure; Carrière, Marie; Collins, Richard; Geoffroy, Nicolas; Carrot, Francine; Covès, Jacques; Gouget, Barbara

2005-01-01

Ralstonia metallidurans CH34, a soil bacterium resistant to a variety of metals, is known to reduce selenite to intracellular granules of elemental selenium (Se0). We have studied the kinetics of selenite (SeIV) and selenate (SeVI) accumulation and used X-ray absorption spectroscopy to identify the accumulated form of selenate, as well as possible chemical intermediates during the transformation of these two oxyanions. When introduced during the lag phase, the presence of selenite increased the duration of this phase, as previously observed. Selenite introduction was followed by a period of slow uptake, during which the bacteria contained Se0 and alkyl selenide in equivalent proportions. This suggests that two reactions with similar kinetics take place: an assimilatory pathway leading to alkyl selenide and a slow detoxification pathway leading to Se0. Subsequently, selenite uptake strongly increased (up to 340 mg Se per g of proteins) and Se0 was the predominant transformation product, suggesting an activation of selenite transport and reduction systems after several hours of contact. Exposure to selenate did not induce an increase in the lag phase duration, and the bacteria accumulated approximately 25-fold less Se than when exposed to selenite. SeIV was detected as a transient species in the first 12 h after selenate introduction, Se0 also occurred as a minor species, and the major accumulated form was alkyl selenide. Thus, in the present experimental conditions, selenate mostly follows an assimilatory pathway and the reduction pathway is not activated upon selenate exposure. These results show that R. metallidurans CH34 may be suitable for the remediation of selenite-, but not selenate-, contaminated environments. PMID:15870319

Immunostimulatory activities of a decapeptide derived from Alcaligenes faecalis FY-3 to crucian carp.

PubMed

Wang, G-X; Li, F-Y; Cui, J; Wang, Y; Liu, Y-T; Han, J; Lei, Y

2011-07-01

A strain was isolated from a soil sample collected from Weihe river in Shaanxi province (108°03'E 34°14'N), which was identified as Alcaligenes faecalis by 16S rRNA analysis. A compound M showing potent immune activity was isolated from secondary metabolites of the strain through bioassay-guided isolation techniques. The structure of the compound M was elucidated using FT-IR, EI-MS, 1H NMR and 13C NMR spectra and identified as cyclo-(L-Pro-Gly)5 which was first time reported as a natural product. We evaluated the immune effects of the cyclo-(L-Pro-Gly)5 on the basis of serum lysozyme activity, bacterial agglutination titre assay, superoxide anion production and phagocytic activity assay, and they were found to be significantly increased by cyclo-(L-Pro-Gly)5. The effects of cyclo-(L-Pro-Gly)5 on immune-related gene expression were further investigated. The outcomes of real-time quantitative polymerase chain reaction (RQ-PCR) proved that the transcribing level of interleukin 6β (IL-6β) and inducible nitric oxide synthase 1β (iNOS-1β) mRNA in the blood leucocytes have been augmented by cyclo-(L-Pro-Gly)5. The challenge experiment showed that crucian carp injected the cyclo-(L-Pro-Gly)5 had significantly (P < 0.05) lower cumulative mortality (13.0%) compared with the control (45.4%) after infection with live Aeromonas hydrophila. These results suggested that cyclo-(L-Pro-Gly)5 is a possible immunostimulant and may strengthen the immune response and protect the heath status of crucian carp against A. hydrophila. © 2011 The Authors. Scandinavian Journal of Immunology © 2011 Blackwell Publishing Ltd.

Replacement of Tyrosine 181 by Phenylalanine in Gentisate 1,2-Dioxygenase I from Pseudomonas alcaligenes NCIMB 9867 Enhances Catalytic Activities

PubMed Central

Tan, Chew Ling; Yeo, Chew Chieng; Khoo, Hoon Eng; Poh, Chit Laa

2005-01-01

xlnE, encoding gentisate 1,2-dioxygenase (EC 1.13.11.4), from Pseudomonas alcaligenes (P25X) was mutagenized by site-directed mutagenesis. The mutant enzyme, Y181F, demonstrated 4-, 3-, 6-, and 16-fold increases in relative activity towards gentisate and 3-fluoro-, 4-methyl-, and 3-methylgentisate, respectively. The specific mutation conferred a 13-fold higher catalytic efficiency (kcat/Km) on Y181F towards 3-methylgentisate than that of the wild-type enzyme. PMID:16237038

Biodegradation of 4-chlorophenol by adsorptive immobilized Alcaligenes sp. A 7-2 in soil.

PubMed

Balfanz, J; Rehm, H J

1991-08-01

Alcaligenes sp. A 7-2 immobilized on granular clay has been applied in a percolator to degrade 4-chlorophenol in sandy soil. Good adsorption rates on granular clay were achieved using cell suspensions with high titres and media at pH 8.0. The influence of various parameters such as aeration rate, pH, temperature, concentration of 4-chlorophenol and size of inoculum on the degradation rate were investigated. During fed-batch fermentations under optimal culture conditions, concentrations of 4-chlorophenol up to 160 mg.l-1 could be degraded. Semicontinuous culture experiments demonstrated that the degradation potential in soil could be well established and enhanced by the addition of immobilized bacteria. Continuous fermentation was performed with varying 4-chlorophenol concentrations in the feed and different input levels. The maximum degradation rate was 1.64 g.l-1.day-1.

Interannual Variability and Trends of CH4, CO and OH Using the Computationally-Efficient CH4-CO-OH (ECCOH) Module

NASA Technical Reports Server (NTRS)

Elshorbany, Yasin F.; Duncan, Bryan N.; Strode, Sarah A.; Wang, James S.; Kouatchou, Jules

2015-01-01

Methane (CH4) is the second most important anthropogenic greenhouse gas (GHG). Its 100-year global warming potential (GWP) is 34 times larger than that for carbon dioxide. The 100-year integrated GWPof CH4 is sensitive to changes in hydroxyl radical (OH) levels.Oxidation of CH4 and carbon monoxide (CO) by OH is the main loss process, thus affecting the oxidizing capacity of the atmosphere and contributing to the global ozone background. Limitations of using archived, monthly OH fields for studies of methane's and COs evolution are that feedbacks of the CH4-CO-OH system on methane, CO and OH are not captured. In this study, we employ the computationally Efficient CH4-CO-OH (ECCOH) module (Elshorbany et al., 2015) to investigate the nonlinear feedbacks of the CH4-CO-OH system on the interannual variability and trends of the CH4, CO, OH system.

Unusual structural phase transition in [N(C2H5)4][N(CH3)4][ZnBr4

NASA Astrophysics Data System (ADS)

Krawczyk, Monika K.; Ingram, Adam; Cach, Ryszard; Czapla, Zbigniew; Czupiński, Olaf; Dacko, Sławomir; Staniorowski, Piotr

2018-04-01

The new hybrid organic-inorganic crystal [N(C2H5)4][N(CH3)4][ZnBr4] was grown and its physical properties and structural phase transition are presented. On the basis of thermal analysis (DSC (differential scanning calorimetry), DTA (differential thermal analysis), DTG), X-ray structural, dilatometric and dielectric studies as well as optical observation, the reversible first-order phase transition at 490/488 K on heating and cooling run, respectively, has been found. An appearance of domain structure of ferroelastic type gives evidence for an untypical lowering of crystal symmetry during the phase transition. At room temperature, the satisfying crystal structure solution was found in the tetragonal system, in the P?21m space group.

ALMA Observations of the IRDC Clump G34.43+00.24 MM3: Complex Organic and Deuterated Molecules

NASA Astrophysics Data System (ADS)

Sakai, Takeshi; Yanagida, Takahiro; Furuya, Kenji; Aikawa, Yuri; Sanhueza, Patricio; Sakai, Nami; Hirota, Tomoya; Jackson, James M.; Yamamoto, Satoshi

2018-04-01

We have observed complex organic molecules (COMs) and deuterated species toward a hot core/corino (HC) associated with the infrared dark cloud clump G34.43+00.24 MM3 with the Atacama Large Millimeter/submillimeter Array. We have detected six normal-COMs (CH3OH, CH3CHO, CH3CH2CN, CH3OCH3, HCOOCH3, and NH2CHO), one deuterated-COM (CH2DCN), and two deuterated fundamental molecules (D2CO and DNC) toward G34.43+00.24 MM3 HC. None of these lines, except for CH3OH, are detected toward the shocked regions in our data, which suggests that COMs do not originate in shocks. The abundance of the COMs relative to CH3OH in G34.43+00.24 MM3 HC is found to be similar to those in high-mass hot cores, rather than those in hot corinos in low-mass star-forming regions. This result suggests that the physical conditions of the warm-up phase of G34.43+00.24 MM3 HC are similar to those of high-mass sources. On the other hand, the D2CO abundance relative to CH3OH in G34.43+00.24 MM3 HC is higher than that of other hot cores, and seems to be comparable to that of hot corinos. The relatively high D2CO/CH3OH ratio of G34.43+00.24 MM3 HC implies a long cold starless phase of G34.43+00.24 MM3 HC.

Biodegradation of ochratoxin A by Alcaligenes faecalis isolated from soil.

PubMed

Zhang, H H; Wang, Y; Zhao, C; Wang, J; Zhang, X L

2017-09-01

The aim of this study is to report on the hydrolytic action of Alcaligenes faecalis isolated from soil samples and its ability to degrade ochratoxin A. An A. faecalis strain was identified and characterized by employing both a phenotypic analysis and 16S rDNA sequence analysis. The results show that this strain could degrade ochratoxin A efficiently but could not use it as a sole carbon source. Ochratoxin α was confirmed as a degradation product in the intracellular extract of A. faecalis using UPLC-MS/MS. Our results suggest that the biodegradation of ochratoxin A by the A. faecalis strain occurs through the hydrolysis of the ochratoxin A amide bond by a putative peptidase. This is the first report to date on the degradation of ochratoxin A by A. faecalis. The A. faecalis strain is presumably a suitable candidate for use in the biodegradation of ochratoxin A. Ochratoxin A, which is produced by some filamentous fungi, severely impacts human and animal health by contaminating several types of food and feed. Our study contributes to the identification of the function of A. faecalis 0D-1, which is capable of producing hydrolytic enzyme(s) to biodegrade ochratoxin A into nontoxic ochratoxin α, to minimize the risk associated with ochratoxin A exposure. © 2017 The Society for Applied Microbiology.

CH-TRU Waste Content Codes

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

Washington TRU Solutions LLC

2008-01-16

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled

Phenoxyacetic acid degradation by the 2,4-dichlorophenoxyacetic acid (TFD) pathway of plasmid pJP4: mapping and characterization of the TFD regulatory gene, tfdR.

PubMed Central

Harker, A R; Olsen, R H; Seidler, R J

1989-01-01

Plasmid pJP4 enables Alcaligenes eutrophus JMP134 to degrade 3-chlorobenzoate and 2,4-dichlorophenoxyacetic acid (TFD). Plasmid pRO101 is a derivative of pJP4 obtained by insertion of Tn1721 into a nonessential region of pJP4. Plasmid pRO101 was transferred by conjugation to several Pseudomonas strains and to A. eutrophus AEO106, a cured isolate of JMP134. AEO106(pRO101) and some Pseudomonas transconjugants grew on TFD. Transconjugants with a chromosomally encoded phenol hydroxylase also degraded phenoxyacetic acid (PAA) in the presence of an inducer of the TFD pathway, namely, TFD or 3-chlorobenzoate. A mutant of one such phenol-degrading strain, Pseudomonas putida PPO300(pRO101), grew on PAA as the sole carbon source in the absence of inducer. This isolate carried a mutant plasmid, designated pRO103, derived from pRO101 through the deletion of a 3.9-kilobase DNA fragment. Plasmid pRO103 constitutively expressed the TFD pathway, and this allowed the metabolism of PAA in the absence of the inducer, TFD. Complementation of pRO103 in trans by a DNA fragment corresponding to the fragment deleted in pRO101 indicates that a negative control-regulatory gene (tfdR) is located on the BamHI E fragment of pRO101. Other subcloning experiments resulted in the cloning of the tfdA monooxygenase gene on a 3.5-kilobase fragment derived from pRO101. This subclone, in the absence of other pRO101 DNA, constitutively expressed the tfdA gene and allowed PPO300 to grow on PAA. Preliminary evidence suggests that the monooxygenase activity encoded by this DNA fragment is feedback-inhibited by phenols. Images PMID:2914848

Detection of OH stretching mode of CH3OH chemisorbed on Ni3+ and Ni4+ by infrared photodissociation spectroscopy.

PubMed

Hirabayashi, Shinichi; Okawa, Ryuji; Ichihashi, Masahiko; Kondow, Tamotsu; Kawazoe, Yoshiyuki

2007-08-09

Structures of nickel cluster ions adsorbed with methanol, Ni3+ (CH3OH)m (m = 1-3) and Ni4+ (CH3OH)m (m = 1-4) were investigated by using infrared photodissociation (IR-PD) spectroscopy based on a tandem-type mass spectrometer, where they were produced by passing Ni3,4+ through methanol vapor under a multiple collision condition. The IR-PD spectra were measured in the wavenumber region between 3100 and 3900 cm-1. In each IR-PD spectrum, a single peak was observed at a wavenumber lower by approximately 40 cm-1 than that of the OH stretching vibration of a free methanol molecule and was assigned to the OH stretching vibrations of the methanol molecules in Ni3,4+ (CH3OH)m. The photodissociation was analyzed by assuming that Ni3,4+ (CH3OH)m dissociate unimolecularly after the photon energy absorbed by them is statistically distributed among the accessible modes of Ni3,4+ (CH3OH)m. In comparison with the calculations performed by the density functional theory, it is concluded that (1) the oxygen atom of each methanol molecule is bound to one of the nickel atoms in Ni3,4+ (defined as molecular chemisorption), (2) the methanol molecules in Ni3,4+ (CH3OH)m do not form any hydrogen bonds, and (3) the cross section for demethanation [CH4 detachment from Nin+ (CH3OH)] is related to the electron density distribution inside the methanol molecule.

Regulation of the cnr Cobalt and Nickel Resistance Determinant from Ralstonia sp. Strain CH34†

PubMed Central

Grass, Gregor; Große, Cornelia; Nies, Dietrich H.

2000-01-01

Ralstonia sp. strain CH34 is resistant to nickel and cobalt cations. Resistance is mediated by the cnr determinant located on plasmid pMOL28. The cnr genes are organized in two clusters, cnrYXH and cnrCBA. As revealed by reverse transcriptase PCR and primer extension, transcription from these operons is initiated from promoters located upstream of the cnrY and cnrC genes. These two promoters exhibit conserved sequences at the −10 (CCGTATA) and −35 (CRAGGGGRAG) regions. The CnrH gene product, which is required for expression of both operons, is a sigma factor belonging to the sigma L family, whose activity seems to be governed by the membrane-bound CnrY and CnrX gene products in response to Ni2+. Half-maximal activation from the cnrCBA operon was determined by using appropriate lacZ gene fusions and was shown to occur at an Ni2+ concentration of about 50 μM. PMID:10671463

2,4-Dichlorophenoxyacetic acid-degrading bacteria contain mosaics of catabolic genes.

PubMed Central

Fulthorpe, R R; McGowan, C; Maltseva, O V; Holben, W E; Tiedje, J M

1995-01-01

DNA from 32 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria from diverse locations was probed with the first three genes of the well-known 2,4-D degradation pathway found in Alcaligenes eutrophus JMP134(pJP4). The majority of strains did not show high levels of homology to the first three genes of the 2,4-D degradation pathway, tfdA, -B, and -C. Most strains showed combinations of tfdA-, B-, and C-like elements that exhibited various degrees of homology to the gene probes. Strains having the same genomic fingerprints (as determined by repetitive extragenic palindromic PCR) exhibited the same hybridization pattern regardless of the geographic origin of the strain, with the exception of a strain isolated from Puerto Rico. This strain had the same genomic fingerprint as that of numerous other strains in the collection but differed in its hybridization against the tfdA gene probe. Members of the beta subdivision of the Proteobacteria class, specifically Alcaligenes, Burkholderia, and Rhodoferax species, carried DNA fragments with 60% or more sequence similarity to tfdA of pJP4, and most carried fragments showing at least 60% homology to tfdB. However, many strains did not hybridize with tfdC, although they exhibited chlorocatechol dioxygenase activity. Members of the alpha subdivision of the Proteobacteria class, mostly of the genus Sphingomonas, did not hybridize to either tfdA or tfdC, but some hybridized at low stringency to tfdB. The data suggest that extensive interspecies transfer of a variety of homologous degradative genes has been involved in the evolution of 2,4-D-degrading bacteria. PMID:7574638

N2O and N2 production during heterotrophic nitrification by Alcaligenes faecalis strain NR.

PubMed

Zhao, Bin; An, Qiang; He, Yi Liang; Guo, Jin Song

2012-07-01

A heterotrophic nitrifier, strain NR, was isolated from a membrane bioreactor. Strain NR was identified as Alcaligenes faecalis by Auto-Microbic system and 16S rRNA gene sequence analysis. A. faecalis strain NR shows a capability of heterotrophic nitrification and N(2)O and N(2) production as well under the aerobic condition. Further tests demonstrated that neither nitrite nor nitrate could be denitrified aerobically by strain NR. However, when hydroxylamine was used as the sole nitrogen source, nitrogenous gases were detected. With an enzyme assay, a 0.063 U activity of hydroxylamine oxidase was observed, while nitrate reductase and nitrite reductase were undetectable. Thus, nitrogenous gas was speculated to be produced via hydroxylamine. Therefore, two different metabolic pathways might exist in A. faecalis NR. One is heterotrophic nitrification by oxidizing ammonium to nitrite and nitrate. The other is oxidizing ammonium to nitrogenous gas directly via hydroxylamine. Copyright © 2012 Elsevier Ltd. All rights reserved.

Helicopter Flying Qualities Characteristics-CH-46E. Volume 1

DTIC Science & Technology

1983-10-03

STABILITY 54 6.0 CONTROL SENSITIVITY 61 . ° i CONTENTS (continued) Page 7.0 TIME HISTORY DATA 65 7.1 GENERAL 65 7.2 DYNAMIC STABILITY 65 7.3 CONTROL...The CH-46E meets these requirements by comfortable margins at the conditions tested. 61 NADC-81118-60 Volume 1 CH-46E (FRB, CONTROL IESPON!SE CH-46E...0 4.- ip L% t ,. _ 5&#34 * ,.4 ••t, EFIGURE 7-5 I 7 ----- 1 FIU- - IA2 NADC-81118-6 Volume I-- .4 . > b in Zh. JI - ag4A 19-- O e t’ c 4 a I,- t

ALMA Detection of Interstellar Methoxymethanol (CH3OCH2OH)

NASA Astrophysics Data System (ADS)

McGuire, Brett A.; Shingledecker, Christopher N.; Willis, Eric R.; Burkhardt, Andrew M.; El-Abd, Samer; Motiyenko, Roman A.; Brogan, Crystal L.; Hunter, Todd R.; Margulès, Laurent; Guillemin, Jean-Claude; Garrod, Robin T.; Herbst, Eric; Remijan, Anthony J.

2017-12-01

We report the detection of interstellar methoxymethanol (CH3OCH2OH) in Atacama Large Millimeter/submillimeter Array (ALMA) Bands 6 and 7 toward the MM1 core in the high-mass star-forming region NGC 6334I at ∼0.″1–1″ spatial resolution. A column density of 4(2) × 1018 cm‑2 at T ex = 200 K is derived toward MM1, ∼34 times less abundant than methanol (CH3OH), and significantly higher than predicted by astrochemical models. Probable formation and destruction pathways are discussed, primarily through the reaction of the CH3OH photodissociation products, the methoxy (CH3O) and hydroxymethyl (CH2OH) radicals. Finally, we comment on the implications of these mechanisms on gas-phase versus grain-surface routes operative in the region, and the possibility of electron-induced dissociation of CH3OH rather than photodissociation.

The Impact of Space Flight on Survival and Interaction of Cupriavidus metallidurans CH34 with Basalt, a Volcanic Moon Analog Rock

PubMed Central

Byloos, Bo; Coninx, Ilse; Van Hoey, Olivier; Cockell, Charles; Nicholson, Natasha; Ilyin, Vyacheslav; Van Houdt, Rob; Boon, Nico; Leys, Natalie

2017-01-01

Microbe-mineral interactions have become of interest for space exploration as microorganisms could be used to biomine from extra-terrestrial material and extract elements useful as micronutrients in life support systems. This research aimed to identify the impact of space flight on the long-term survival of Cupriavidus metallidurans CH34 in mineral water and the interaction with basalt, a lunar-type rock in preparation for the ESA spaceflight experiment, BIOROCK. Therefore, C. metallidurans CH34 cells were suspended in mineral water supplemented with or without crushed basalt and send for 3 months on board the Russian FOTON-M4 capsule. Long-term storage had a significant impact on cell physiology and energy status (by flow cytometry analysis, plate count and intracellular ATP measurements) as 60% of cells stored on ground lost their cell membrane potential, only 17% were still active, average ATP levels per cell were significantly lower and cultivability dropped to 1%. The cells stored in the presence of basalt and exposed to space flight conditions during storage however showed less dramatic changes in physiology, with only 16% of the cells lost their cell membrane potential and 24% were still active, leading to a higher cultivability (50%) and indicating a general positive effect of basalt and space flight on survival. Microbe-mineral interactions and biofilm formation was altered by spaceflight as less biofilm was formed on the basalt during flight conditions. Leaching from basalt also changed (measured with ICP-OES), showing that cells release more copper from basalt and the presence of cells also impacted iron and magnesium concentration irrespective of the presence of basalt. The flight conditions thus could counteract some of the detrimental effects observed after the 3 month storage conditions. PMID:28503167

The Impact of Space Flight on Survival and Interaction of Cupriavidus metallidurans CH34 with Basalt, a Volcanic Moon Analog Rock.

PubMed

Byloos, Bo; Coninx, Ilse; Van Hoey, Olivier; Cockell, Charles; Nicholson, Natasha; Ilyin, Vyacheslav; Van Houdt, Rob; Boon, Nico; Leys, Natalie

2017-01-01

Microbe-mineral interactions have become of interest for space exploration as microorganisms could be used to biomine from extra-terrestrial material and extract elements useful as micronutrients in life support systems. This research aimed to identify the impact of space flight on the long-term survival of Cupriavidus metallidurans CH34 in mineral water and the interaction with basalt, a lunar-type rock in preparation for the ESA spaceflight experiment, BIOROCK. Therefore, C. metallidurans CH34 cells were suspended in mineral water supplemented with or without crushed basalt and send for 3 months on board the Russian FOTON-M4 capsule. Long-term storage had a significant impact on cell physiology and energy status (by flow cytometry analysis, plate count and intracellular ATP measurements) as 60% of cells stored on ground lost their cell membrane potential, only 17% were still active, average ATP levels per cell were significantly lower and cultivability dropped to 1%. The cells stored in the presence of basalt and exposed to space flight conditions during storage however showed less dramatic changes in physiology, with only 16% of the cells lost their cell membrane potential and 24% were still active, leading to a higher cultivability (50%) and indicating a general positive effect of basalt and space flight on survival. Microbe-mineral interactions and biofilm formation was altered by spaceflight as less biofilm was formed on the basalt during flight conditions. Leaching from basalt also changed (measured with ICP-OES), showing that cells release more copper from basalt and the presence of cells also impacted iron and magnesium concentration irrespective of the presence of basalt. The flight conditions thus could counteract some of the detrimental effects observed after the 3 month storage conditions.

Mass spectrometric identification of Au68(SR)34 molecular gold nanoclusters with 34-electron shell closing.

PubMed

Dass, Amala

2009-08-26

The molecular formula Au(68)(SCH(2)CH(2)Ph)(34) has been assigned to the 14 kDa nanocluster using MALDI-TOF mass spectrometry. The 34-electron shell closing in a macroscopically obtained thiolated gold nanocluster is demonstrated. The Au(68) nanocluster is predicted to have a 49 atom Marks decahedral core with 19 inner core atoms and 30 outer atoms chelating with the staple motifs. The nanoclusters' predicted formulation is [Au](19+30) [Au(SR)(2)](11) [Au(2)(SR)(3)](4).

The C-H Stretching Features at 3.2--3.5 μm of Polycyclic Aromatic Hydrocarbons with Aliphatic Sidegroups

NASA Astrophysics Data System (ADS)

Yang, X. J.; Li, Aigen; Glaser, R.; Zhong, J. X.

2016-07-01

The so-called “unidentified” infrared emission (UIE) features at 3.3, 6.2, 7.7, 8.6, and 11.3 μm are ubiquitously seen in a wide variety of astrophysical regions. The UIE features are characteristic of the stretching and bending vibrations of aromatic hydrocarbon materials, e.g., polycyclic aromatic hydrocarbon (PAH) molecules. The 3.3 μm aromatic C-H stretching feature is often accompanied by a weaker feature at 3.4 μm. The latter is generally thought to result from the C-H stretch of aliphatic groups attached to the aromatic systems. The ratio of the observed intensity of the 3.3 μm aromatic C-H feature to that of the 3.4 μm aliphatic C-H feature allows one to estimate the aliphatic fraction of the UIE carriers, provided that the intrinsic oscillator strengths of the 3.3 μm aromatic C-H stretch ({A}3.3) and the 3.4 μm aliphatic C-H stretch ({A}3.4) are known. While previous studies on the aliphatic fraction of the UIE carriers were mostly based on the {A}3.4/{A}3.3 ratios derived from the mono-methyl derivatives of small PAH molecules, in this work we employ density functional theory to compute the infrared vibrational spectra of PAH molecules with a wide range of sidegroups including ethyl, propyl, butyl, and several unsaturated alkyl chains, as well as all the isomers of dimethyl-substituted pyrene. We find that, except for PAHs with unsaturated alkyl chains, the corresponding {A}3.4/{A}3.3 ratios are close to that of mono-methyl PAHs. This confirms the predominantly aromatic nature of the UIE carriers previously inferred from the {A}3.4/{A}3.3 ratio derived from mono-methyl PAHs.

The kinetic study of hydrogen bacteria and methanotrophs in pure and defined mixed cultures

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

Arora, D.K.

The kinetics of pure and mixed cultures of Alcaligenes eutrophus H 16 and Methylobacterium organophilum CRL 26 under double substrate limited conditions were studied. In pure culture growth kinetics, a non-interactive model was found to fit the experimental data best. The yield of biomass on limiting substrate was found to vary with the dilution rate. The variation in the biomass yield may be attributed to the change in metabolic pathways resulting from a shift in the limiting substrates. Both species exhibited wall growth in the chemostat under dark conditions. However, under illuminated conditions, there was significant reduction in wall growth.more » Poly-{beta}-hydroxybutyric acid was synthesized by both species under ammonia and oxygen limiting conditions. The feed gas mixture was optimized to achieve the steady-state coexistence of these two species in a chemostate for the first time. In mixed cultures, the biomass species assays were differentiated on the basis of their selective growth on particular compounds: Sarcosine and D-arabinose were selected for hydrogen bacteria and methylotrophs, respectively. The kinetics parameters estimated from pure cultures were used to predict the growth kinetics of these species in defined mixed cultures.« less

C-H Hot Bands in the Near-IR Emission Spectra of Leonids

NASA Technical Reports Server (NTRS)

Freund, F. T.; Scoville, J.; Holm, R.; Seelemann, R.; Freund, M. M.

2002-01-01

The reported infrared (IR) emission spectra from 1999 Leonid fireballs show a 3.4 micron C-H emission band and unidentified bands at longer wavelengths. Upon atmospheric entry, the Leonid meteorites were flash-heated to temperatures around 2400K, which would destroy any organics on the surface of the meteorite grains. We propose that the nu(sub )CH emission band in the Leonid emission spectra arises from matrix-embedded C(sub n)-H-O entities that are protected from instant pyrolysis. Our model is based on IR absorption nu(sub )CH bands, which we observed in laboratory-grown MgO and natural olivine single crystals, where they arise from C(sub n)-H-O units imbedded in the mineral matrix, indicative of aliphatic -CH2- and -CH3 organics. Instead of being pyrolyzed, the C(sub n)-H-O entities in the Leonid trails become vibrationally excited to higher levels n = 1, 2, 3 etc. During de-excitation they emit at 3.4 microns, due to the (0 => 1) transition, and at longer wavelengths, due to hot bands. As a first step toward verifying this hypothesis we measured the C-H vibrational manifold of hexane (C6H14). The calculated positions of the (2 => l ) , (3 => 2), and possibly (4 => 3) hot bands agree with the Leonid emission bands at 3.5, 3.8 and 4.l microns.

Integrated systems for biopolymers and bioenergy production from organic waste and by-products: a review of microbial processes.

PubMed

Pagliano, Giorgia; Ventorino, Valeria; Panico, Antonio; Pepe, Olimpia

2017-01-01

Recently, issues concerning the sustainable and harmless disposal of organic solid waste have generated interest in microbial biotechnologies aimed at converting waste materials into bioenergy and biomaterials, thus contributing to a reduction in economic dependence on fossil fuels. To valorize biomass, waste materials derived from agriculture, food processing factories, and municipal organic waste can be used to produce biopolymers, such as biohydrogen and biogas, through different microbial processes. In fact, different bacterial strains can synthesize biopolymers to convert waste materials into valuable intracellular (e.g., polyhydroxyalkanoates) and extracellular (e.g., exopolysaccharides) bioproducts, which are useful for biochemical production. In particular, large numbers of bacteria, including Alcaligenes eutrophus , Alcaligenes latus , Azotobacter vinelandii , Azotobacter chroococcum , Azotobacter beijerincki , methylotrophs, Pseudomonas spp., Bacillus spp., Rhizobium spp., Nocardia spp., and recombinant Escherichia coli , have been successfully used to produce polyhydroxyalkanoates on an industrial scale from different types of organic by-products. Therefore, the development of high-performance microbial strains and the use of by-products and waste as substrates could reasonably make the production costs of biodegradable polymers comparable to those required by petrochemical-derived plastics and promote their use. Many studies have reported use of the same organic substrates as alternative energy sources to produce biogas and biohydrogen through anaerobic digestion as well as dark and photofermentation processes under anaerobic conditions. Therefore, concurrently obtaining bioenergy and biopolymers at a reasonable cost through an integrated system is becoming feasible using by-products and waste as organic carbon sources. An overview of the suitable substrates and microbial strains used in low-cost polyhydroxyalkanoates for biohydrogen and biogas

Temperature-Dependent Kinetics Studies of the Reactions Br((sup 2)P3/2) + H2S yields SH + HBr and Br((sup 2)P3/2) + CH3SH yields CH3S + HBr. Heats of Formation of SH and CH3S Radicals

NASA Technical Reports Server (NTRS)

Nicovich, J. M.; Kreutter, K. D.; vanDijk, C. A.; Wine, P. H.

1997-01-01

Time resolved resonance fluorescence detection of Br(sup 2)P3/2) atom disappearance or appearance following 266-nm laser flash photolysis of CF2Br2/H2S/H2/N2, CF2Br2/CH3SH/H2/N2, Cl2CO/H2S/HBr/N2, and CH3SSCH3/HBr/H2/N2 mixtures has been employed to study the kinetics of the reactions Br((sup 2)P3/2) + H2S = SH + HBr (1,-1) and Br((sup2)P3/2) + CH3SH = CH3S + HBr (2, -2) as a function of temperature over the range 273-431K. Arrhenius expressions in units of 10(exp -12) cu cm/molecule/s which describe the results are k1 = (14.2 +/- 3.4) exp[(-2752 +/- 90)/T],(k-1) = (4.40 +/- 0.92) exp[(-971 +/- 73)/T],k(2) = (9.24 +/- 1.15) exp[(-386 +/- 41)/T], and k(-2) = (1.46 +/-0.21) exp[(-399 +/-41)/T; errors are 2 sigma and represent precision only. By examining Br((sup 2)P3/2) equilibrium kinetics following 355nm laser flash photolysis of Br2/CH3SH/H2/N2 mixtures, a 298 K rate coefficient of (1.7 +/- 0.5) x 10(exp -10) cu cm/molecule/s has been obtained for the reaction CH3S + Br2 yields CH3SBr + Br. To our knowledge, these are the first kinetic data reported for each of the reactions studied. Measured rate coefficients, along with known rate coefficients for similar radical + H2S, CH3SH, HBr,Br2 reactions are considered in terms of possible correlations of reactivity with reaction thermochemistry and with IP - EA, the difference between the ionization potential of the electron donor and the electron affinity of the electron acceptor. Both thermochemical and charge-transfer effects appear to be important in controlling observed reactivities. Second and third law analyses of the equilibrium data for reactions 1 and 2 have been employed to obtain the following enthalpies of reaction in units of kcal/mol: for reaction 1, Delta-H(298) = 3.64 +/- 0.43 and Delta-H(0) = 3.26 +/-0.45; for reaction 2, Delta-H(298) = -0.14 +/- 0.28 and Delta-H(0) = -0.65 +/- 0.36. Combining the above enthalpies of reaction with the well-known heats of formation of Br, HBr, H2S, and CH3SH gives the

Solid state coordination chemistry: structural consequences of variations in tether length in the oxovanadium-copper-bisterpy-[O3P(CH2)nPO3]4- system, n= 1-6 (bisterpy = 2,2':4',4'':2'',2'''-quarterpyridyl-6',6''-di-2-pyridine).

PubMed

Ouellette, Wayne; Koo, Bon-Kweon; Burkholder, Eric; Golub, Vladimir; O'Connor, C J; Zubieta, Jon

2004-05-21

Hydrothermal reactions of Na3VO4, an appropriate Cu(II) source, bisterpy and an organodiphosphonate, H2O3P(CH2)nPO3H2 (n = 1-6) yielded a family of materials of the type [Cu2(bisterpy)]4+/VxOy(n-)/[O3P(CH2)nPO3]4-. This family of bimetallic oxides is characterized by an unusual structural diversity. The oxides [[Cu2(bisterpy)]V2O4[O3PCH2PO3H]2] (1), [[Cu2(bisterpy)(H2O)]VO2[O3P(CH2)3PO3][HO3P(CH2)3PO3H2

Louisiana SIP: LAC 33:III Ch 2147. Limiting Volatile Organic Compound (VOC) Emissions from Reactor Processes and Distillation Operations in Synthetic Organic Chemical manufacturing Industry (SOCMI); SIP effective 2011-08-04 (LAd34) to 2017-09-27

EPA Pesticide Factsheets

Louisiana SIP: LAC 33:III Ch 2147. Limiting Volatile Organic Compound (VOC) Emissions from Reactor Processes and Distillation Operations in Synthetic Organic Chemical manufacturing Industry (SOCMI); SIP effective 2011-08-04 (LAd34) to 2017-09-27

Production of poly-beta-hydroxybutyrate (PHB) by Alcaligenes latus from maple sap.

PubMed

Yezza, Abdessalem; Halasz, Annamaria; Levadoux, Wayne; Hawari, Jalal

2007-11-01

Maple sap, an abundant natural product especially in Canada, is rich in sucrose and thus may represent an ideal renewable feedstock for the production of a wide variety of value-added products. In the present study, maple sap or sucrose was employed as a carbon source to Alcaligenes latus for the production of poly-beta-hydroxybutyrate (PHB). In shake flasks, the biomass obtained from both the sap and sucrose were 4.4 +/- 0.5 and 2.9 +/- 0.3 g/L, and the PHB contents were 77.6 +/- 1.5 and 74.1 +/- 2.0%, respectively. Subsequent batch fermentation (10 L sap) resulted in the formation of 4.2 +/- 0.3 g/L biomass and a PHB content of 77.0 +/- 2.6%. The number average molecular weights of the PHB produced by A. latus from maple sap and pure sucrose media were 300 +/- 66 x 10(3) and 313 +/- 104 x 10(3) g/mol, respectively. Near-infrared, (1)H magnetic resonance imaging (MRI), and (13)C-MRI spectra of the microbially produced PHB completely matched those obtained with a reference material of poly[(R)-3-hydroxybutyric acid]. The polymer was found to be optically active with [alpha](25) (D) equaled to -7.87 in chloroform. The melting point (177.0 degrees C) and enthalpy of fusion (77.2 J/g) of the polymer were also in line with those reported, i.e., 177 degrees C and 81 J/g, respectively.

Thermodynamics of ligand binding to histone deacetylase like amidohydrolase from Bordetella/Alcaligenes.

PubMed

Meyners, Christian; Baud, Matthias G J; Fuchter, Matthew J; Meyer-Almes, Franz-Josef

2014-03-01

Thermodynamic studies on ligand-protein binding have become increasingly important in the process of drug design. In combination with structural data and molecular dynamics simulations, thermodynamic studies provide relevant information about the mode of interaction between compounds and their target proteins and therefore build a sound basis for further drug optimization. Using the example of histone deacetylases (HDACs), particularly the histone deacetylase like amidohydrolase (HDAH) from Bordetella/Alcaligenes, a novel sensitive competitive fluorescence resonance energy transfer-based binding assay was developed and the thermodynamics of interaction of both fluorescent ligands and inhibitors to histone deacetylase like amidohydrolase were investigated. The assay consumes only small amounts of valuable target proteins and is suitable for fast kinetic and mechanistic studies as well as high throughput screening applications. Binding affinity increased with increasing length of aliphatic spacers (n = 4-7) between the hydroxamate moiety and the dansyl head group of ligand probes. Van't Hoff plots revealed an optimum in enthalpy contribution to the free energy of binding for the dansyl-ligand with hexyl spacer. The selectivity in the series of dansyl-ligands against human class I HDAC1 but not class II HDACs 4 and 6 increased with the ratio of ΔH(0)/ΔG(0). The data clearly emphasize the importance of thermodynamic signatures as useful general guidance for the optimization of ligands or rational drug design. Copyright © 2014 John Wiley & Sons, Ltd.

Louisiana SIP: LAC 33:III Ch. 7 Section 701. Purpose and Information Regarding Standards for PM10, SO2, CO, Atmospheric Oxidants, NOx and Pb; SIP effective 1989-05-08 (LAc49) to 2011-08-03 (LAd34 - Revised)

EPA Pesticide Factsheets

Louisiana SIP: LAC 33:III Ch. 7 Section 701. Purpose and Information Regarding Standards for PM10, SO2, CO, Atmospheric Oxidants, NOx and Pb; SIP effective 1989-05-08 (LAc49) to 2011-08-03 (LAd34 - Revised)

Louisiana SIP: LAC 33:III Ch 2132. Stage II Vapor Recovery Systems for Control of Vehicle Refuelling Emissions at Gasoline Dispensing Facilities; SIP effective 2011-08-04 (LAd34) and 2016-02-29 (LAd47) to 2017-09-27

EPA Pesticide Factsheets

Louisiana SIP: LAC 33:III Ch 2132. Stage II Vapor Recovery Systems for Control of Vehicle Refuelling Emissions at Gasoline Dispensing Facilities; SIP effective 2011-08-04 (LAd34) and 2016-02-29 (LAd47) to 2017-09-27

Microbial remediation of soils co-contaminated with 2,4-dichlorophenoxyacetic acid and cadmium

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

Roane, T.M.; Pepper, I.L.

1997-12-31

One-third of organically-polluted sites are also contaminated with metals; however, the bioremediation potential of such sites is not clear. While metals are thought to inhibit the abilities of microbial communities to degrade organic pollutants, several microbial-metal resistance mechanisms are known to exist. This study utilizes cadmium-resistant soil microorganisms to enhance the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) in the presence of cadmium. Cadmium-resistant bacteria were isolated from both a 40-year-old metal-contaminated soil and an uncontaminated soil. During growth experiments, it was found that the uncontaminated soil had a greater number of resistant isolates at low concentrations of cadmium, while the cadmium-contaminatedmore » soil exhibited higher microbial resistance with increased cadmium concentrations. ERIC PCR fingerprints discriminated among the cadmium-resistant isolates identified by BIOLOG as Bacillus, Corynecbacterium, Pseudomonas, and Xanthomonas spp. These isolates were resistant to concentrations ranging from 5 to 275 ppm soluble cadmium. In conventional degradation studies, two resistant isolates, a Bacillus and an unidentified Gram positive rod, supported the degradation of 500 ppm 2,4-D by the cadmium-sensitive 2,4-D degrader Alcaligenes eutrophus JMP134 in the presence of 20 and 40 ppm soluble cadmium, respectively.« less

Kinetics of OH- and Cl-initiated oxidation of CH2dbnd CHC(O)O(CH2)2CH3 and CH2dbnd CHCH2C(O)O(CH2)2CH3 and fate of the alkoxy radicals formed

NASA Astrophysics Data System (ADS)

Rivela, Cynthia; Blanco, María B.; Teruel, Mariano A.

2016-05-01

Rate coefficients of the reactions of OH and Cl radicals with vinyl and allyl butyrate were determined for the first time at 298 K and 1 atm using the relative method to be (in cm3 molecule-1 s-1): k1(OH + CH2dbnd CHC(O)O(CH2)2CH3) = (2.61 ± 0.31) × 10-11, k2(Cl + CH2dbnd CHC(O)O(CH2)2CH3) = (2.48 ± 0.89) × 10-10, k3(OH + CH2dbnd CHCH2C(O)O(CH2)2CH3) = (2.89 ± 0.31) × 10-11, and k4(Cl + CH2dbnd CHCH2C(O)O(CH2)2CH3) = (2.25 ± 0.96) × 10-10. Reactivity trends and atmospheric lifetimes of esters are presented. Additionally, a product study shown butyric acid and polifunctional products for the reactions of vinyl and allyl butyrate, respectively and general mechanism is proposed.

Tentative detection of ethylene glycol toward W51/e2 and G34.3+0.2 ⋆⋆⋆

NASA Astrophysics Data System (ADS)

Lykke, J. M.; Favre, C.; Bergin, E. A.; Jørgensen, J. K.

2015-10-01

Context. With only a few low- and high-mass star-formation regions studied in detail so far, it is unclear what role the enviroment plays in complex molecule formation. In this light, a comparison of relative abundances of related species between sources might be useful for explaining any observed differences. Aims: We seek to measure the relative abundance between three important complex organic molecules, ethylene glycol ((CH2OH)2), glycolaldehyde (CH2OHCHO) and methyl formate (HCOOCH3), toward high-mass protostars and thereby provide additional constraints on their formation pathways. Methods: We use IRAM 30 m single-dish observations of the three species toward two high-mass star-forming regions - W51/e2 and G34.3+0.2 - and report a tentative detection of (CH2OH)2 toward both sources. Results: Assuming that (CH2OH)2, CH2OHCHO, and HCOOCH3 spatially coexist, relative abundance ratios, HCOOCH3/(CH2OH)2, of 31 and 35 are derived for G34.3+0.2 and W51/e2, respectively. CH2OHCHO is not detected, but the data provide lower limits to the HCOOCH3/CH2OHCHO abundance ratios of ≥193 for G34.3+0.2 and ≥550 for W51/e2. A comparison of these results to measurements from various sources in the literature indicates that the source luminosities may be correlated with the HCOOCH3/(CH2OH)2 and HCOOCH3/CH2OHCHO ratios. This apparent correlation may be a consequence of the relative time scales each source spend at different temperature ranges in their evolution. Furthermore, we obtain lower limits to the ratio of (CH2OH)2/CH2OHCHO for G34.3+0.2 (≥6) and W51/e2 (≥16). This result confirms that a high (CH2OH)2/CH2OHCHO abundance ratio is not a specific property of comets, as previously speculated. Based on observations carried out with the IRAM 30 m telescope.The reduced spectra (FITS files) are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/582/A64Appendices are available in

Photosynthates as dominant source of CH4 and CO2 in soil water and CH4 emitted to the atmosphere from paddy fields

NASA Astrophysics Data System (ADS)

Minoda, Tomomi; Kimura, Mamoto; Wada, Eitaro

1996-09-01

Emission rates of CH4 from paddy soil with and without rice straw applications were measured with pot experiments to estimate the contribution of rice straw to the total CH4 emission during the growth period of rice plants. The CH4 derived from rice straw was calculated to be 44% of the total emission. 13CO2 uptake experiments were also carried out four times from June 30 to September 13, 1994, to estimate the contribution of photosynthesized carbon to CH4 emission. The contribution percentages of photosynthesized carbon to the total CH4 emitted to the atmosphere were 3.8% around June 30, 31% around July 25, 30% around August 19, and 14% around September 13 in the treatment with rice straw applications, and 52% around July 25, 28% around August 19, and 15% around September 13 in the treatment without rice straw applications. They were calculated to be 22% and 29% for the entire growth period in the treatments with and without rice straw applications, respectively. The contribution percentages of photosynthesized carbon to the total CH4 and inorganic carbon (Σ CO2) dissolved in soil water were 1.3%, 30%, 29%, and 34% for dissolved CH4 and 3.0%, 36%, 30% and 28% for dissolved inorganic carbon around June 30, July 25, August l9, and September 13, respectively, in the treatment with rice straw applications. They were 70%, 23%, and 32% for dissolved CH4 and 31%, 16%, and 19% for dissolved inorganic carbon around July 25, August 19, and September 13, respectively, in the treatment without rice straw applications.

Potential of Cupriavidus metallidurans CH34 for in situ resource utilization from basalt by determining the molecular micro-mineral interactions

NASA Astrophysics Data System (ADS)

Byloos, Bo; Van Houdt, Rob; Boon, Nico; Leys, Natalie

In order to maintain a persistent human presence in space, materials must either be provided from Earth or generated from material already present in space, in a process referred to as 'in situ resource utilization (ISRU)'. Microorganisms can biomine useful elements from extra-terrestrial materials for use as nutrients in a life support system or to aid in the creation of soil. To effectively use bacteria in an ISRU process more needs to be known about the molecular mechanisms behind microbe-mineral interaction and the influence of microgravity and radiation that affect bioleaching. The aim of this research project is to define the microbe-mineral interactions on basalt, which is a major constituent of Lunar or Martian regolith, the mechanisms that are important in bioleaching and how this process will be altered by space flight conditions. In particular, the research will be focussed on the determination of the genes and proteins involved in the biosynthesis of metallophores and exopolysaccharides (EPS), and biofilm formation. Iron, copper and phosphate uptake mechanisms are investigated in detail because these have been shown to be essential for life and bacteria are faced with limitation of these nutrients in the environment. In this study the bacterium Cupriavidus metallidurans CH34 is used to study these interactions. C. metallidurans CH34 is a soil bacterium which is resistant to up to 20 different heavy metal ions. Its behaviour in space has already been determined with earlier flight experiments to the ISS. It was recently discovered that C. metallidurans forms a biofilm and is capable of leaching calcium, magnesium and iron from basalt to sustain its growth First, C. metallidurans was grown in conditions with and without basalt, iron, copper and phosphate and the production of EPS and metallophores was examined. The iron, copper and phosphate concentrations which are limiting and optimal to allow C. metallidurans cell proliferation could be determined as

Unimolecular reactivity of organotrifluoroborate anions, RBF3- , and their alkali metal cluster ions, M(RBF3 )2- (M = Na, K; R = CH3 , CH3 CH2 , CH3 (CH2 )3 , CH3 (CH2 )5 , c-C3 H5 , C6 H5 , C6 H5 CH2 , CH2 CHCH2 , CH2 CH, C6 H5 CO).

PubMed

Bathie, Fiona L B; Bowen, Chris J; Hutton, Craig A; O'Hair, Richard A J

2018-07-15

Potassium organotrifluoroborates (RBF 3 K) are important reagents used in organic synthesis. Although mass spectrometry is commonly used to confirm their molecular formulae, the gas-phase fragmentation reactions of organotrifluoroborates and their alkali metal cluster ions have not been previously reported. Negative-ion mode electrospray ionization (ESI) together with collision-induced dissociation (CID) using a triple quadrupole mass spectrometer were used to examine the fragmentation pathways for RBF 3 - (where R = CH 3 , CH 3 CH 2 , CH 3 (CH 2 ) 3 , CH 3 (CH 2 ) 5 , c-C 3 H 5 , C 6 H 5 , C 6 H 5 CH 2 , CH 2 CHCH 2 , CH 2 CH, C 6 H 5 CO) and M(RBF 3 ) 2 - (M = Na, K), while density functional theory (DFT) calculations at the M06/def2-TZVP level were used to examine the structures and energies associated with fragmentation reactions for R = Me and Ph. Upon CID, preferentially elimination of HF occurs for RBF 3 - ions for systems where R = an alkyl anion, whereas R - formation is favoured when R = a stabilized anion. At higher collision energies loss of F - and additional HF losses are sometimes observed. Upon CID of M(RBF 3 ) 2 - , formation of RBF 3 - is the preferred pathway with some fluoride transfer observed only when M = Na. The DFT-calculated relative thermochemistry for competing fragmentation pathways is consistent with the experiments. The main fragmentation pathways of RBF 3 - are HF elimination and/or R - loss. This contrasts with the fragmentation reactions of other organometallate anions, where reductive elimination, beta hydride transfer and bond homolysis are often observed. The presence of fluoride transfer upon CID of Na(RBF 3 ) 2 - but not K(RBF 3 ) 2 - is in agreement with the known fluoride affinities of Na + and K + and can be rationalized by Pearson's HSAB theory. Copyright © 2018 John Wiley & Sons, Ltd.

ChIP-seq.

PubMed

Kim, Tae Hoon; Dekker, Job

2018-05-01

Owing to its digital nature, ChIP-seq has become the standard method for genome-wide ChIP analysis. Using next-generation sequencing platforms (notably the Illumina Genome Analyzer), millions of short sequence reads can be obtained. The densities of recovered ChIP sequence reads along the genome are used to determine the binding sites of the protein. Although a relatively small amount of ChIP DNA is required for ChIP-seq, the current sequencing platforms still require amplification of the ChIP DNA by ligation-mediated PCR (LM-PCR). This protocol, which involves linker ligation followed by size selection, is the standard ChIP-seq protocol using an Illumina Genome Analyzer. The size-selected ChIP DNA is amplified by LM-PCR and size-selected for the second time. The purified ChIP DNA is then loaded into the Genome Analyzer. The ChIP DNA can also be processed in parallel for ChIP-chip results. © 2018 Cold Spring Harbor Laboratory Press.

ChIP and ChIP-Related Techniques: Expanding the Fields of Application and Improving ChIP Performance.

PubMed

Visa, Neus; Jordán-Pla, Antonio

2018-01-01

Protein-DNA interactions in vivo can be detected and quantified by chromatin immunoprecipitation (ChIP). ChIP has been instrumental for the advancement of epigenetics and has set the groundwork for the development of a number of ChIP-related techniques that have provided valuable information about the organization and function of genomes. Here, we provide an introduction to ChIP and discuss the applications of ChIP in different research areas. We also review some of the strategies that have been devised to improve ChIP performance.

Ice core δD(CH4) record precludes marine hydrate CH4 emissions at the onset of Dansgaard-Oeschger events

NASA Astrophysics Data System (ADS)

Bock, M.; Schmitt, J.; Möller, L.; Spahni, R.; Blunier, T.; Fischer, H.

2010-12-01

Air enclosures in polar ice cores represent the only direct paleoatmospheric archive (besides firn air) and show that atmospheric CH4 concentrations changed in concert with northern hemisphere temperature during both glacial/interglacial transitions as well as rapid climate changes (Dansgaard-Oeschger events). For stadials and interstadials during Marine Isotope Stage 3 concentration jumps of 100 - 200 ppbv within a few decades are observed. A concentration gradient with higher values in the northern versus the southern hemisphere during warm stages was reconstructed from ice core methane data from Greenland and Antarctica. This gradient indicates additional methane emissions during warm periods located in the northern hemisphere. However, the underlying processes for these changes are still not well understood. With tropical and boreal wetlands, biomass burning, thermokarst lakes, ruminants, termites, UV-induced emissions from organic matter and marine gas hydrates all contributing to the natural atmospheric CH4 level, an unambiguous source attribution remains difficult. Also changes in the methane sinks can modify the tropospheric CH4 budget, as trace gases like volatile organic compounds are competing for the major reactant - the OH radical. Additionally, the changing global atmospheric methane concentration itself feeds back on its lifetime. Together with the CH4 interhemispheric gradient, stable hydrogen and carbon isotopic studies on methane (δD(CH4) and δ13CH4) in ice cores allow to constrain individual CH4 source/sink changes. Here we present clear evidence from the North Greenland Ice Core Project ice core based on the hydrogen isotopic composition of methane δD(CH4) that clathrates did not cause atmospheric methane concentration to rise at the onset of Dansgaard-Oeschger (DO) events 7 and 8 (34 - 41 kilo years before present), however, we can not exclude that they played a minor role during and at the end of an interstadial. Box modeling supports

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

PubMed Central

2010-01-01

Background Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome. Results We have developed ChIPpeakAnno as a Bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions. The binding sites annotated with ChIPpeakAnno can be viewed easily as a table, a pie chart or plotted in histogram form, i.e., the distribution of distances to the nearest genes for each set of peaks. In addition, we have implemented functionalities for determining the significance of overlap between replicates or binding sites among transcription factors within a complex, and for drawing Venn diagrams to visualize the extent of the overlap between replicates. Furthermore, the package includes functionalities to retrieve sequences flanking putative binding sites for PCR amplification, cloning, or motif discovery, and to identify Gene Ontology (GO) terms associated with adjacent genes. Conclusions ChIPpeakAnno enables batch annotation of the binding sites identified from ChIP-seq, ChIP-chip, CAGE or any technology that results in a large number of enriched genomic regions within the statistical programming environment R. Allowing users to pass their own annotation data such

Selenium carboxylic acids betaine; 3,3‧,3″-selenotris(propanoic acid) betaine, Se(CH2CH2COOH)2(CH2CH2COO)

NASA Astrophysics Data System (ADS)

Doudin, Khalid; Törnroos, Karl W.

2017-06-01

Attempts to prepare [Se(CH2CH2COOH)3]+Cl- from Se(CH2CH2COOH)2 and H2Cdbnd CHCOOH in concentrated hydrochloric acid, for the corresponding sulfonium salt, led exclusively to the Se-betaine, Se(CH2CH2COOH)2(CH2CH2COO). The Se-betaine crystallises in the space group P2l/c with the cell dimensions at 223 K, a = 5.5717(1), b = 24.6358(4), c = 8.4361(1) Å, β = 104.762(1)°, V = 1119.74(3) Å3, Z = 4, Dcalc = 1.763 Mgm- 3, μ = 3.364 Mm-1. The structure refined to RI = 0.0223 for 2801 reflections with Fo > 4σ(Fo). In the crystalline state the molecule is intermolecularly linked to neighbouring molecules by a number of hydrogen bonds; a very strong carboxylic-carboxylate bond with an O⋯O distance of 2.4435(16) Å, a medium strong carboxylic-carboxylate bond with an O⋯O distance of 2.6431(16) Å and several weak O⋯H(CH2) with O⋯C distances between 3.2 and 3.3 Å. In the carboxylic group involved in the very strong hydrogen bond the O⋯H bond is antiperiplanar to the Cdbnd O bond while the Osbnd H bond is periplanar to the Cdbnd O bond in the second carboxylic group. Based upon the Csbnd O bond lengths and the elongation of the Osbnd H bond involved in the strong hydrogen bond one may describe the compound as strongly linked units of Se(CH2CH2COOH)(CH2CH2COO)2 rather than Se(CH2CH2COOH)2(CH2CH2COO). The selenium atom forms two strong intramolecular 1,5-Se⋯O contacts, with a carboxylate oxygen atom, 2.9385(12) Å, and with a carboxylic oxygen atom, 2.8979(11) Å. To allow for these contacts the two organic fragments have been forced into the periplanar conformation. The molecule is only slightly asymmetric with regard to the Csbnd Sesbnd C bond angles but is very asymmetric with regard to the torsion angles.

Antimicrobial activity and determination of bioactive components from marine Alcaligenes faecalis extract against a sulfate-reducing bacteria

NASA Astrophysics Data System (ADS)

AbdSharad, Ali; Usup, Gires; Sahrani, Fathul Karim; Ahmad, Asmat

2016-11-01

Biogenic souring and microbial-influenced corrosion is a common scenario in petroleum reservoir. The serious threat normally comes from sulfate-reducing bacteria (SRB). Alcaligenes faecalis was tested in this study for the ability to inhibit the growth of SRB. Ethyl acetate extraction of A. faecalis grown in marine broth was carried out to produce crude ethyl acetate of A. faecalis (CEAF). CEAF was diluted at concentrations 0.2-12.8 mg/mL and was tested for anti-microbial activity by microdilution susceptibility tests in 96-wells plate. CEAF was then analyzed by Gas Chromatography Mass Spectrometry (GC-MS). The microdilution susceptibility tests showed that the crude have anti- microbial activities on SRB. CEAF showed immediate killing effect against SRB in liquid medium which suggest the presence of active chemical compounds with antimicrobial activity. The GC-MS analysis showed the presence of 20 different chemical compounds in CEAF, The major components in CEAF can be related to antimicrobial, antifungal, antioxidant, pesticide, metabolism, toxicity, anticancer and corrosion inhibition activities. In conclusion, crude ethyl acetate extract of A. faecalis has the ability to inhibit SRB growth.

Laboratory Spectroscopy of CH(+) and Isotopic CH

NASA Technical Reports Server (NTRS)

Pearson, John C.; Drouin, Brian J.

2006-01-01

The A1II - X1(Epsilon) electronic band of the CH(+) ion has been used as a probe of the physical and dynamical conditions of the ISM for 65 years. In spite of being one of the first molecular species observed in the ISM and the very large number of subsequent observations with large derived column densities, the pure rotational spectra of CH+ has remained elusive in both the laboratory and in the ISM as well. We report the first laboratory measurement of the pure rotation of the CH(+) ion and discuss the detection of CH-13(+) in the ISM. Also reported are the somewhat unexpected chemical conditions that resulted in laboratory production.

Wheat Bran Enhances the Cytotoxicity of Immobilized Alcaligenes aquatilis F8 against Microcystis aeruginosa

PubMed Central

Sun, Pengfei; Lin, Hui; Wang, Guan; Zhang, Ximing; Zhang, Qichun; Zhao, Yuhua

2015-01-01

Algicidal bacteria offer a promising option for killing cyanobacteria. Therefore, a new Alcaligenes aquatilis strain F8 was isolated to control Microcystis aeruginosa in this study. The algicidal activity of strain F8 was dependent on the cell density of M. aeruginosa, and the maximal algicidal rate of the free bacterium reached 88.45% within 72 h. With a view to its application to the control of M. aeruginosa in the natural environment, strain F8 was immobilized in sodium alginate beads, but immobilization of the strain decreased its algicidal rate compared to that of the free bacterium. However, addition of wheat bran to the sodium alginate matrix used to immobilize strain F8 not only eliminated the adverse effects of immobilization on the bacteria but also resulted in an 8.83% higher algicidal rate of the immobilized than free bacteria. Exclusion and recovery methods were used to identify key ingredients of wheat bran and gain insight into the mechanism underlying the observed enhancement of algicidal activity. This analysis indicated that certain factors in wheat bran, including vitamins B1, B2, B9, and E were responsible for promoting bacterial growth and thereby improving the algicidal rate of immobilized strain F8. Our findings indicate that wheat bran is able to improve the algicidal efficiency of A. aquatilis strain F8 for killing M. aeruginosa and is a good source of not only carbon and nitrogen but also vitamins for bacteria. PMID:26295573

libChEBI: an API for accessing the ChEBI database.

PubMed

Swainston, Neil; Hastings, Janna; Dekker, Adriano; Muthukrishnan, Venkatesh; May, John; Steinbeck, Christoph; Mendes, Pedro

2016-01-01

ChEBI is a database and ontology of chemical entities of biological interest. It is widely used as a source of identifiers to facilitate unambiguous reference to chemical entities within biological models, databases, ontologies and literature. ChEBI contains a wealth of chemical data, covering over 46,500 distinct chemical entities, and related data such as chemical formula, charge, molecular mass, structure, synonyms and links to external databases. Furthermore, ChEBI is an ontology, and thus provides meaningful links between chemical entities. Unlike many other resources, ChEBI is fully human-curated, providing a reliable, non-redundant collection of chemical entities and related data. While ChEBI is supported by a web service for programmatic access and a number of download files, it does not have an API library to facilitate the use of ChEBI and its data in cheminformatics software. To provide this missing functionality, libChEBI, a comprehensive API library for accessing ChEBI data, is introduced. libChEBI is available in Java, Python and MATLAB versions from http://github.com/libChEBI, and provides full programmatic access to all data held within the ChEBI database through a simple and documented API. libChEBI is reliant upon the (automated) download and regular update of flat files that are held locally. As such, libChEBI can be embedded in both on- and off-line software applications. libChEBI allows better support of ChEBI and its data in the development of new cheminformatics software. Covering three key programming languages, it allows for the entirety of the ChEBI database to be accessed easily and quickly through a simple API. All code is open access and freely available.

Model-Based Nutrient Feeding Strategies for the Increased Production of Polyhydroxybutyrate (PHB) by Alcaligenes latus.

PubMed

Gahlawat, Geeta; Srivastava, Ashok K

2017-10-01

Polyhydroxyalkanoates (PHAs) are biodegradable polymers which are considered as an effective alternative for conventional plastics due to their mechanical properties similar to the latter. However, the widespread use of these polymers is still hampered due to their higher cost of production as compared to plastics. The production cost could be overcome by obtaining high yields and productivity. The goal of the present research was to enhance the yield of polyhydroxybutyrate (PHB) with the help of two simple fed-batch cultivation strategies. In the present study, average batch kinetic and substrate limitation/inhibition study data of Alcaligenes latus was used for the development of PHB model which was then adopted for designing various off-line nutrient feeding strategies to enhance PHB accumulation. The predictive ability of the model was validated by experimental implementation of two fed-batch strategies. One such dynamic strategy of fed-batch cultivation under pseudo-steady state with respect to nitrogen and simultaneous carbon feeding strategy resulted in significantly high biomass and PHB concentration of 39.17 g/L and 29.64 g/L, respectively. This feeding strategy demonstrated a high PHB productivity and PHB content of 0.6 g/L h and 75%, respectively, which were remarkably high in comparison to batch cultivation. The mathematical model can also be employed for designing various other nutrient feeding strategies.

Flowing afterglow studies of the electron recombination of protonated cyanides (RCN)H+ and their proton-bound dimer ions (RCN)2H+ where R is H, CH3, and CH3CH2

NASA Astrophysics Data System (ADS)

McLain, J. L.; Molek, C. D.; , D. Osborne, Jr.; Adams, N. G.

2009-05-01

A study has been made of the electron-ion dissociative recombination of the protonated cyanides (RCNH+, R = H, CH3, C2H5) and their proton-bound dimers (RCN)2H+ at 300 K. This has been accomplished with the flowing afterglow technique using an electrostatic Langmuir probe to determine the electron density decay along the flow tube. For the protonated species, the recombination coefficients, [alpha]e(cm3 s-1), are (3.6 +/- 0.5) × 10-7, (3.4 +/- 0.5) × 10-7, (4.6 +/- 0.7) × 10-7 for R = H, CH3, C2H5, respectively. For the proton-bound dimers, the [alpha]e are substantially greater being (2.4 +/- 0.4) × 10-6, (2.8 +/- 0.4) × 10-6, (2.3 +/- 0.3) × 10-6 for R = H, CH3, C2H5, respectively. Fitting of the electron density decay data to a simple model has shown that the rate coefficients for the three-body association of RCNH+ with RCN are very large being (2.0 +/- 0.5) × 10-26 cm6 s-1. The significance of these data to the Titan ionosphere is discussed.

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

PubMed Central

Carroll, Thomas S.; Liang, Ziwei; Salama, Rafik; Stark, Rory; de Santiago, Ines

2014-01-01

With the advent of ChIP-seq multiplexing technologies and the subsequent increase in ChIP-seq throughput, the development of working standards for the quality assessment of ChIP-seq studies has received significant attention. The ENCODE consortium's large scale analysis of transcription factor binding and epigenetic marks as well as concordant work on ChIP-seq by other laboratories has established a new generation of ChIP-seq quality control measures. The use of these metrics alongside common processing steps has however not been evaluated. In this study, we investigate the effects of blacklisting and removal of duplicated reads on established metrics of ChIP-seq quality and show that the interpretation of these metrics is highly dependent on the ChIP-seq preprocessing steps applied. Further to this we perform the first investigation of the use of these metrics for ChIP-exo data and make recommendations for the adaptation of the NSC statistic to allow for the assessment of ChIP-exo efficiency. PMID:24782889

Louisiana SIP: LAC 33:III Ch 23 Subchap B, §2303--Aluminum Plants, §2303 Standards for Horizontal Stud Soderberg Primary Aluminum Plants and Prebake Primary Aluminum Plants; SIP effective 1989-05-08 (LAc49) to 2011-08-03 (LAad34 - Revised)

EPA Pesticide Factsheets

Louisiana SIP: LAC 33:III Ch 23 Subchap B, §2303--Aluminum Plants, §2303 Standards for Horizontal Stud Soderberg Primary Aluminum Plants and Prebake Primary Aluminum Plants; SIP effective 1989-05-08 (LAc49) to 2011-08-03 (LAad34 - Revised)

The interstellar C-H stretching band near 3.4 microns - Constraints on the composition of organic material in the diffuse interstellar medium

NASA Technical Reports Server (NTRS)

Sandford, S. A.; Allamandola, L. J.; Tielens, A. G. G. M.; Pendleton, Y.; Sellgren, K.

1991-01-01

The composition and history of dust in the diffuse ISM was studied using 3600-2700/cm absorption spectra of objects which have widely varying amounts of visual extinctions along different lines of sight. The 3300/cm and 2950/cm features are attributed to O-H and C-H stretching vibrations, respectively. The O-H feature in OH 32.8-0.3 is suggestive of circumstellar water ice and is probably not due to material in the diffuse ISM. The features in the 3100-2700/cm region are attributed either to C-H vibrations or to M stars. The spectra of the latter show a series of narrow features in this region that are identified with photospheric OH. Objects in which these bands are seen include OH 01-477, T629-5, and the Galactic center source IRS 7. The C-H stretch feature of diffuse ISM dust has subpeaks which fall within 5/cm of C-H stretching vibrations in the -CH2- and -CH3 groups of saturated aliphatic hydrocarbons.

Polycyclic Aromatic Hydrocarbons with Aliphatic Sidegroups: Intensity Scaling for the C-H Stretching Modes and Astrophysical Implications

NASA Astrophysics Data System (ADS)

Yang, X. J.; Li, Aigen; Glaser, R.; Zhong, J. X.

2017-03-01

The so-called unidentified infrared emission (UIE) features at 3.3, 6.2, 7.7, 8.6, and 11.3 μ {{m}} ubiquitously seen in a wide variety of astrophysical regions are generally attributed to polycyclic aromatic hydrocarbon (PAH) molecules. Astronomical PAHs may have an aliphatic component, as revealed by the detection in many UIE sources of the aliphatic C-H stretching feature at 3.4 μ {{m}}. The ratio of the observed intensity of the 3.4 μ {{m}} feature to that of the 3.3 μ {{m}} aromatic C-H feature allows one to estimate the aliphatic fraction of the UIE carriers. This requires knowledge of the intrinsic oscillator strengths of the 3.3 μ {{m}} aromatic C-H stretch ({A}3.3) and the 3.4 μ {{m}} aliphatic C-H stretch ({A}3.4). Lacking experimental data on {A}3.3 and {A}3.4 for the UIE candidate materials, one often has to rely on quantum-chemical computations. Although the second-order Møller-Plesset (MP2) perturbation theory with a large basis set is more accurate than the B3LYP density functional theory, MP2 is computationally very demanding and impractical for large molecules. Based on methylated PAHs, we show here that, by scaling the band strengths computed at an inexpensive level (e.g., B3LYP/6-31G*), we are able to obtain band strengths as accurate as those computed at far more expensive levels (e.g., MP2/6-311+G(3df,3pd)). We calculate the model spectra of methylated PAHs and their cations excited by starlight of different spectral shapes and intensities. We find that {({I}3.4/{I}3.3)}{mod}, the ratio of the model intensity of the 3.4 μ {{m}} feature to that of the 3.3 μ {{m}} feature, is insensitive to the spectral shape and intensity of the exciting starlight. We derive a straightforward relation for determining the aliphatic fraction of the UIE carriers (I.e., the ratio of the number of C atoms in aliphatic units {N}{{C},{ali}} to that in aromatic rings {N}{{C},{aro}}) from the observed band ratios {({I}3.4/{I}3.3)}{obs}: {N

On the Jupiter's ephemeris in the Ch'i-Yao Jang-Tsai-Chüch.

NASA Astrophysics Data System (ADS)

Niu, Weixing; Jiang, Xiaoyuan

Jupiter's ephemeris preserved in the Ch'i-Yao Jang-Tsai-Chüch is interpreted. Then the time and position coordinates of Jupiter's first stationary point, second stationary point, first visibility in the east and last visibility in the west, which recorded in the ephemeris are analysed. The accuracy of the ephemeris is also discussed. Finally, it is identified that the ephemeris has been used as an astrological handbook by Japanese astrologers in 973 - 1132.

Rate constants for the reactions of OH with CH3Cl, CH2Cl2, CHCl3, and CH3Br

NASA Technical Reports Server (NTRS)

Hsu, K.-J.; Demore, W. B.

1994-01-01

Rate constants for the reactions of OH with CH3Cl, CH2Cl2, CHCl3, and CH3Br have been measured by a relative rate technique in which the reaction rate of each compound was compared to that of HFC-152a (CH3CHF2) and (for CH2Cl2) HFC-161 (CH3CH2F). Using absolute rate constants for HFC-152a and HFC-161, which we have determined relative to those for CH4, CH3CCl3, and C2H6, temperature dependent rate constants of both compounds were derived. The derived rate constant for CH3Br is in good agreement with recent absolute measurements. However, for the chloromethanes all the rate constants are lower at atmospheric temperatures than previously reported, especially for CH2Cl2 where the present rate constant is about a factor of 1.6 below the JPL 92-20 value. The new rate constant appears to resolve a discrepancy between the observed atmospheric concentrations and those calculated from the previous rate constant and estimated release rates.

Microbial degradation of 2,4-dichlorophenoxyacetic acid: Insight into the enzymes and catabolic genes involved, their regulation and biotechnological implications.

PubMed

Kumar, Ajit; Trefault, Nicole; Olaniran, Ademola Olufolahan

2016-01-01

A considerable progress has been made to understand the mechanisms of biodegradation of 2,4-dichlorophenoxyacetic acid (2,4-D). 2,4-D biodegradation pathway has been elucidated in many microorganisms including Cupriavidus necator JMP134 (previously known as Wautersia eutropha, Ralstonia eutropha and Alcaligenes eutrophus) and Pseudomonas strains. It generally involves the side chain removal of 2,4-D by α-ketoglutarate-dependent 2,4-D dioxygenase (tfdA) to form 2,4-dichlorophenol (2,4-DCP); hydroxylation of 2,4-DCP by 2,4-DCP hydroxylase (tfdB) to form dichlorocatechol; ortho or meta cleavage of dichlorocatechol by chlorocatechol 1,2-dioxygenase (tfdC) to form 2,4-dichloro-cis,cis-muconate; conversion of 2,4-dichloro-cis,cis-muconate to 2-chlorodienelactone by chloromuconate cycloisomerase (tfdD); conversion of 2-chlorodienelactone to 2-chloromaleylacetate by chlorodienelactone hydrolase (tfdE) and, finally, conversion of 2-chloromaleylacetate to 3-oxoadepate via maleylacetate by chloromaleylacetate reductase and maleylacetate reductase (tfdF), respectively, which is funnelled to the tricarboxylic acid cycle. The latest review on microbial breakdown of 2,4-D, other halogenated aromatic pesticides, and related compounds was compiled by Haggblom, however, a considerable progress has been made in this area of research since then. Thus, this review focuses on the recent advancement on 2,4-D biodegradation, the enzymes, and genes involved and their biotechlogical implications.

Direct Production of Propene from the Thermolysis of Poly(..beta..-hydroxybutyrate)

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

Mittal, Ashutosh; Pilath, Heidi M.; Johnson, David K.

To transform biomass components into hydrocarbon fuels it is clear that there are two main transformations that need to occur, i.e., deoxygenation and carbon chain extension. The potential routes for decreasing the oxygen content of biomass intermediates include dehydration, hydrodeoxygenation and decarboxylation. One route that is examined here is the conversion of polyhydroxyalkanoates (PHA) to alkenes that would be intermediates to hydrocarbon fuels.Thermal breakdown of PHA proceeds via an intermediate carboxylic acid, which can then be decarboxylated to an alkene. Oligomerization of alkenes by well-known commercial technologies would permit production of a range of hydrocarbon fuels from a carbohydrate derivedmore » intermediate. Moreover, polyhydroxybutyrate (PHB) can be produced in Cupriavidus necator (formerly known as Ralstonia eutropha) and Alcaligenes eutrophus on a variety of carbon sources including glucose, fructose and glycerol with PHB accumulation reaching 75 percent of dry cell mass. We conducted thermal conversion of PHB and pure crotonic acid (CA), the intermediate carboxylic acid produced by thermal depolymerization of PHB, in a flow-through reactor. The results of initial experiments on the thermal conversion of CA showed that up to 75 mole percent yields of propene could be achieved by optimizing the residence time and temperature of the reactor. Further experiments are being investigated to optimize the reactor parameters and enhance propene yields via thermal conversion of PHB.« less

Cholinesterase (ChE) response and related mortality among birds fed ChE inhibitors

USGS Publications Warehouse

Ludke, J.L.; Hill, E.F.; Dieter, M.P.

1975-01-01

Patterns of mortality and inhibition of brain and plasma ChE in birds treated with ChE inhibitors were studied in an attempt to determine the validity of using ChE activity as a monitoring and diagnostic technique. Analysis of brain ChE activity proved to be reliable for diagnosing and monitoring effects of selected ChE inhibitors in birds. Brain ChE inhibition exceeding 20% indicated exposure, and inhibition greater than 50% was sufficient for diagnosing cause of death. Individuals that died from dietary exposure to parathion or carbofuran had brain ChE activities below 55% of normal; although individuals could survive with brain ChE activity lower than 50%. Problems associated with collection, storage, and analysis of tissues for ChE activity are discussed.

Production and characterization of poly(3-hydroxybutyrate) generated by Alcaligenes latus using lactose and whey after acid protein precipitation process.

PubMed

Berwig, Karina Hammel; Baldasso, Camila; Dettmer, Aline

2016-10-01

Whey after acid protein precipitation was used as substrate for PHB production in orbital shaker using Alcaligenes latus. Statistical analysis determined the most appropriate hydroxide for pH neutralization of whey after protein precipitation among NH4OH, KOH and NaOH 10%w/v. The results were compared to those of commercial lactose. A scale-up test in a 4L bioreactor was done at 35°C, 750rpm, 7L/min air flow, and 6.5 pH. The PHB was characterized through Fourier Transform Infrared Spectroscopy, thermogravimetry and differential scanning calorimetry. NH4OH provided the best results for productivity (p), 0.11g/L.h, and for polymer yield, (YP/S), 1.08g/g. The bioreactor experiment resulted in lower p and YP/S. PHB showed maximum degradation temperature (291°C), melting temperature (169°C), and chemical properties similar to those of standard PHB. The use of whey as a substrate for PHB production did not affect significantly the final product quality. Copyright © 2016 Elsevier Ltd. All rights reserved.

Louisiana SIP: LAC 33:III Ch. 7 - Table 2 - Ambient Air--Methods of Contaminant Measurements; SIP effective 1989-05-08 (LAc49) and 1989-08-14 (LAc50) to 2011-08-03 (LAd34 - Moved to Section 711 and revised [adds PM-2.5])

EPA Pesticide Factsheets

Louisiana SIP: LAC 33:III Ch. 7 - Table 2 - Ambient Air--Methods of Contaminant Measurements; SIP effective 1989-05-08 (LAc49) and 1989-08-14 (LAc50) to 2011-08-03 (LAd34 - Moved to Section 711 and revised [adds PM-2.5])

Louisiana SIP: LAC 33:III Ch. 7 Section 709. Measurement of Concentrations PM10, SO2, Carbon Monoxide, Atmospheric Oxidants, Nitrogen Oxides, and Lead; SIP effective 1989-05-08 (LAc49) and 1989-08-14 (LAc50) to 2011-08-03 (LAd34 - Revised)

EPA Pesticide Factsheets

Louisiana SIP: LAC 33:III Ch. 7 Section 709. Measurement of Concentrations PM10, SO2, Carbon Monoxide, Atmospheric Oxidants, Nitrogen Oxides, and Lead; SIP effective 1989-05-08 (LAc49) and 1989-08-14 (LAc50) to 2011-08-03 (LAd34 - Revised)

Ice chemistry of acetaldehyde reveals competitive reactions in the first step of the Strecker synthesis of alanine: formation of HO-CH(CH3)-NH2 vs. HO-CH(CH3)-CN

NASA Astrophysics Data System (ADS)

Fresneau, Aurélien; Danger, Grégoire; Rimola, Albert; Duvernay, Fabrice; Theulé, Patrice; Chiavassa, Thierry

2015-08-01

The understanding of compound formation in laboratory simulated astrophysical environments is an important challenge in obtaining information on the chemistry occurring in these environments. We here investigate by means of both laboratory experiments and quantum chemical calculations the ice-based reactivity of acetaldehyde (CH3CHO) with ammonia (NH3) and hydrogen cyanide (HCN) in excess of water (H2O) promoted by temperature. A priori, this study should give information on alanine (2HN-CH(CH3)-COOH) formation (the simplest chiral amino acid detected in meteorites), since these reactions concern the first steps of its formation through the Strecker synthesis. However, infrared spectroscopy, mass spectrometry with HC14N or HC15N isotopologues and B3LYP-D3 results converge to indicate that an H2O-dominated ice containing CH3CHO, NH3 and HCN not only leads to the formation of α-aminoethanol (2HN-CH(CH3)-OH, the product compound of the first step of the Strecker mechanism) and its related polymers (2HN-(CH(CH3)-O)n-H) due to reaction between CH3CHO and NH3, but also to the 2-hydroxypropionitrile (HO­-CH(CH3)-CN) and its related polymers (H-(O-CH(CH3))n-CN) from direct reaction between CH3CHO and HCN. The ratio between these two species depends on the initial NH3/HCN ratio in the ice. Formation of α-aminoethanol is favoured when the NH3 concentration is larger than HCN. We also show that the presence of water is essential for the formation of HO­-CH(CH3)-CN, contrarily to 2HN-CH(CH3)-OH whose formation also takes place in absence of H2O ice. As in astrophysical ices NH3 is more abundant than HCN, formation of α-aminoethanol should consequently be favoured compared to 2-hydroxypropionitrile, thus pointing out α-aminoethanol as a plausible intermediate species for alanine synthesis through the Strecker mechanism in astrophysical ices.

The 3.4 micron emission in comets

NASA Technical Reports Server (NTRS)

Brooke, Tim Y.; Knacke, Roger F.; Owen, T. C.; Tokunaga, Alan T.

1989-01-01

Emission features near 3.4 microns were detected in comet Bradfield (1987s) on 17 Nov. 1987 UT, and, marginally, on two earlier dates, with the Cooled Grating Array Spectrometer at the NASA Infrared Radio Telescope Facility (IRTF) (Brooke et al., 1988b). The central wavelength (3.36 microns) and width (approx. 0.15 microns) of the strongest feature coincide with those observed in comet Halley. A weaker emission feature at 3.52 microns and a strong feature extending shortward of 2.9 microns were also detected. This brings the number of comets in which these three features have been seen to three, two new (Bradfield, Wilson) and one old (Halley). It seems almost certain that the 3.4 micron features are emissions by C-H groups in complex molecules. Based on the similarity of the 3.4 micron features in comets Halley and Wilson, the authors suggest that a particular set of organic compounds may be common to all comets (Brooke et al. 1988a). The absence of the feature in some comets could then be due to photodestruction or evaporation of the organics when the comet approaches the sun, in combination with a predominance of thermal emission from non C-H emitting grains. Detection of the 3.4 micron emission feature in comet Bradfield at 4 = 0.9 AU provides support for this argument. Complex organics in comets could have been formed by particle irradiation of parent ices in the nucleus or been incorporated as grains at the time the comets formed. Since the most heavily irradiated layers of Halley would have been lost in its hundreds of perihelion passages, the authors believe the more likely explanation is that the 3.4 micron emitting material was incorporated in comet nuclei at the time of formation. The 3.4 micron comet feature resembles, but is not identical to, the interstellar 3.29 micron (and longer wavelength) emission features and the broad 3.4 micron feature seen in absorption toward the Galactic center. Detailed comparisons of cometary and interstellar organics

New superhindered polydentate polyphosphine ligands P(CH2CH2P(t)Bu2)3, PhP(CH2CH2P(t)Bu2)2, P(CH2CH2CH2P(t)Bu2)3, and their ruthenium(II) chloride complexes.

PubMed

Gilbert-Wilson, Ryan; Field, Leslie D; Bhadbhade, Mohan M

2012-03-05

The synthesis and characterization of the extremely hindered phosphine ligands, P(CH(2)CH(2)P(t)Bu(2))(3) (P(2)P(3)(tBu), 1), PhP(CH(2)CH(2)P(t)Bu(2))(2) (PhP(2)P(2)(tBu), 2), and P(CH(2)CH(2)CH(2)P(t)Bu(2))(3) (P(3)P(3)(tBu), 3) are reported, along with the synthesis and characterization of ruthenium chloro complexes RuCl(2)(P(2)P(3)(tBu)) (4), RuCl(2)(PhP(2)P(2)(tBu)) (5), and RuCl(2)(P(3)P(3)(tBu)) (6). The bulky P(2)P(3)(tBu) (1) and P(3)P(3)(tBu) (3) ligands are the most sterically encumbered PP(3)-type ligands so far synthesized, and in all cases, only three phosphorus donors are able to bind to the metal center. Complexes RuCl(2)(PhP(2)P(2)(tBu)) (5) and RuCl(2)(P(3)P(3)(tBu)) (6) were characterized by crystallography. Low temperature solution and solid state (31)P{(1)H} NMR were used to demonstrate that the structure of RuCl(2)(P(2)P(3)(tBu)) (4) is probably analogous to that of RuCl(2)(PhP(2)P(2)(tBu)) (5) which had been structurally characterized.

ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis

PubMed Central

Li, Guipeng; Chen, Yang; Snyder, Michael P.; Zhang, Michael Q.

2017-01-01

ChIA-PET2 is a versatile and flexible pipeline for analyzing different types of ChIA-PET data from raw sequencing reads to chromatin loops. ChIA-PET2 integrates all steps required for ChIA-PET data analysis, including linker trimming, read alignment, duplicate removal, peak calling and chromatin loop calling. It supports different kinds of ChIA-PET data generated from different ChIA-PET protocols and also provides quality controls for different steps of ChIA-PET analysis. In addition, ChIA-PET2 can use phased genotype data to call allele-specific chromatin interactions. We applied ChIA-PET2 to different ChIA-PET datasets, demonstrating its significantly improved performance as well as its ability to easily process ChIA-PET raw data. ChIA-PET2 is available at https://github.com/GuipengLi/ChIA-PET2. PMID:27625391

Co-processing CH4 and oxygenates on Mo/H-ZSM-5: 2. CH4-CO2 and CH4-HCOOH mixtures.

PubMed

Bedard, Jeremy; Hong, Do-Young; Bhan, Aditya

2013-08-07

Co-processing of formic acid or carbon dioxide with CH4 (FA/CH4 = 0.01-0.03 and CO2/CH4 = 0.01-0.03) on Mo/H-ZSM-5 catalysts at 950 K with the prospect of kinetically coupling dehydrogenation and deoxygenation cycles results instead in a two-zone, staged bed reactor configuration consisting of upstream oxygenate/CH4 reforming and downstream CH4 dehydroaromatization. The addition of an oxygenate co-feed (oxygenate/CH4 = 0.01-0.03) causes oxidation of the active molybdenum carbide catalyst while producing CO and H2 until completely converted. Forward rates of C6H6 synthesis are unaffected by the introduction of an oxygenate co-feed after rigorously accounting for the thermodynamic reversibility caused by the H2 produced in oxygenate reforming reactions and the fraction of the active catalyst deemed unavailable for CH4 DHA. All effects of co-processing oxygenates with CH4 can be construed in terms of an approach to equilibrium.

Biosorption characteristic of Alcaligenes sp. BAPb.1 for removal of lead(II) from aqueous solution.

PubMed

Jin, Yu; Yu, Sumei; Teng, Chunying; Song, Tao; Dong, Liying; Liang, Jinsong; Bai, Xin; Xu, Xiuhong; Qu, Juanjuan

2017-06-01

In this study, strain BAPb.1 was isolated from lead mining area and used as an adsorbent to remove lead(II) ions from aqueous solution. The physicochemical characteristics, heavy metal resistance and antibiotic sensitivity of strain BAPb.1 were investigated. Biosorption capacity was evaluated by batch biosorption experiments, and isothermal characteristics were discussed. Atomic force microscopy (AFM), scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX) and Fourier transform infrared spectrometry (FTIR) were conducted to explore the mechanism for lead(II) adsorption. Based on morphological and physiological characteristics as well as the phylogenetic analysis of 16S rDNA sequences, strain BAPb.1 was identified as a member of the genus Alcaligenes. It exhibited high resistances to multiple heavy metals such as lead(II), copper(II), zinc(II), nickel(II) and chromium(VI), and to antibiotics such as kanamycin, ampicillin, streptomycin, chloramphenicol, and tetracycline. The optimum conditions for maximum biosorption rate of 85.2% and maximum capacity of 56.8 mg g -1 were found at pH of 5, adsorbent dosage of 1.5 g L -1 (dry weight), initial lead(II) concentration of 100 mg L -1 , and contact time of 30 min at 30 °C. Biosorption isotherms were well fitted with Langmuir isotherm model. Mechanism analysis reveals that the lead(II) ions may exchange with sodium and potassium ions, and the hydroxyl, carbonyl and phosphate groups on the cell surface can chelate the lead(II) ions, therefore, surface adsorption play significant role in the biosorption process.

Inhibition of Serratia marcescens Smj-11 biofilm formation by Alcaligenes faecalis STN17 crude extract

NASA Astrophysics Data System (ADS)

Lutfi, Zainal; Usup, Gires; Ahmad, Asmat

2014-09-01

Serratia marcescens biofilms are formed when they are bound to surfaces in aqueous environments. S. marcescens utilizes N-acylhomoserine lactone (AHL) as its quorum sensing signal molecule. The accumulation of AHL indicates the bacteria to produce matrices to form biofilms. Prodigiosin (2-methyl-3-pentyl-6-methoxyprodigiosin), which causes red pigmentation in the colonies, are also produced when the AHL reaches a certain threshold. The Alcaligenes faecalis STN17 crude extract is believed to inhibit quorum sensing in the S. marcescens Smj-11 and, thus, impedes its biofilm formation ability. A. faecalis STN17 was grown in marine broth, and ethyl acetate extraction was carried out. The crude compound of A. faecalis STN17 was diluted at high concentration (0.2-6.4 mg/mL) and was taken to confirm anti-biofilm activity through the crystal violet method in 96-wells plate. Then, the crude extract underwent purification using simple solvents partitioning test to discern the respective compounds that had the anti-biofilm activity under the crystal violet method. The crystal violet test showed that the crude did have anti-biofilm activity on S. marcescens Smj-11, but did not kill the cells. This finding signifies that the suppression of biofilm formation in S. marcescens by A. faecalis STN17 has a strong correlation. The partitioning test showed that A. faecalis STN17 crude extract has several compounds and only the compound(s) in chloroform showed activities. In conclusion, the crude extract of A. faecalis STN17 has the ability to inhibit S. marcescens Smj-11 biofilm formation.

ChIP-re-ChIP: Co-occupancy Analysis by Sequential Chromatin Immunoprecipitation.

PubMed

Beischlag, Timothy V; Prefontaine, Gratien G; Hankinson, Oliver

2018-01-01

Chromatin immunoprecipitation (ChIP) exploits the specific interactions between DNA and DNA-associated proteins. It can be used to examine a wide range of experimental parameters. A number of proteins bound at the same genomic location can identify a multi-protein chromatin complex where several proteins work together to regulate gene transcription or chromatin configuration. In many instances, this can be achieved using sequential ChIP; or simply, ChIP-re-ChIP. Whether it is for the examination of specific transcriptional or epigenetic regulators, or for the identification of cistromes, the ability to perform a sequential ChIP adds a higher level of power and definition to these analyses. In this chapter, we describe a simple and reliable method for the sequential ChIP assay.

Anharmonic Effect in CH3CH2C(=O)OCH2CH3 Decomposition

NASA Astrophysics Data System (ADS)

Ding, Yang; Song, Liguo; Yao, Li; Xia, Wenwen

2017-12-01

In this paper, using the B3LYP functional and CCSD(T) method with 6-311++G** basis set, the harmonic and anharmonic rate constants in the unimolecular dissociation of ethyl propanoate have been calculated using Rice-Ramsperger-Kassel-Marcus theory. The anharmonic rate constants of the title reaction have also been examined, the comparison shows that, the anharmonic effect especially in the case of high total energies and temperature for channels 3 to 6 is significant, so that the anharmonic effect cannot be neglected for unimolecular dissociation reaction of CH3CH2C(=O)OCH2CH3 both in microcanonical and canonical systems.

ChIP-chip.

PubMed

Kim, Tae Hoon; Dekker, Job

2018-05-01

ChIP-chip can be used to analyze protein-DNA interactions in a region-wide and genome-wide manner. DNA microarrays contain PCR products or oligonucleotide probes that are designed to represent genomic sequences. Identification of genomic sites that interact with a specific protein is based on competitive hybridization of the ChIP-enriched DNA and the input DNA to DNA microarrays. The ChIP-chip protocol can be divided into two main sections: Amplification of ChIP DNA and hybridization of ChIP DNA to arrays. A large amount of DNA is required to hybridize to DNA arrays, and hybridization to a set of multiple commercial arrays that represent the entire human genome requires two rounds of PCR amplifications. The relative hybridization intensity of ChIP DNA and that of the input DNA is used to determine whether the probe sequence is a potential site of protein-DNA interaction. Resolution of actual genomic sites bound by the protein is dependent on the size of the chromatin and on the genomic distance between the probes on the array. As with expression profiling using gene chips, ChIP-chip experiments require multiple replicates for reliable statistical measure of protein-DNA interactions. © 2018 Cold Spring Harbor Laboratory Press.

Louisiana SIP: LAC 33:III Ch 61 Subchap A, §6121 to § 6131--Method 43 - Capture Efficiency Test Procedures; SIP effective 1994-06-06 (LAc60) to to 2011-08-03 (LAd34 - Moved to Chap 21 Subchap N §§ 2155-2160 and revised)

EPA Pesticide Factsheets

Louisiana SIP: LAC 33:III Ch 61 Subchap A, §6121 to § 6131--Method 43 - Capture Efficiency Test Procedures; SIP effective 1994-06-06 (LAc60) to to 2011-08-03 (LAd34 - Moved to Chap 21 Subchap N §§ 2155-2160 and revised)

Luminescent Copper(I) Halide Butterfly Dimers Coordinated to [Au(CH3imCH2py)2]BF4 and [Au(CH3imCH2quin)2]BF4

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

Catalano, V.; Moore, A; Shearer, J

2009-01-01

The coordination chemistry of copper(I) halides to the homoleptic, N-heterocyclic carbene Au(I) complexes [Au(CH{sub 3}imCH{sub 2}quin){sub 2}]BF{sub 4} and [Au(CH{sub 3}imCH{sub 2}py){sub 2}]BF{sub 4} was explored. The reaction of CuX (X = Cl, Br, I) with either [Au(CH{sub 3}imCH{sub 2}quin){sub 2}]BF{sub 4} or [Au(CH{sub 3}imCH{sub 2}py){sub 2}]BF{sub 4} produces trimetallic complexes containing Cu{sub 2}X{sub 2}-butterfly copper clusters coordinated to the two imine moieties. The triangular arrangement of the metals places the gold(I) center in close proximity ({approx}2.5-2.6 {angstrom}) to the centroid of the Cu-Cu vector. The Cu-Cu separations vary as a function of bridging halide with the shortest Cu-Cu separationsmore » of {approx}2.5 {angstrom} found in the iodo-complexes and the longest separations of 2.9 {angstrom} found in the bridging chloride complexes. In all six complexes the Au-Cu separations range from {approx}2.8 to 3.0 {angstrom}. In the absence of halides, the dimetallic complex [AuCu(CH{sub 3}imCH{sub 2}py){sub 2}(NCCH{sub 3}){sub 2}](BF{sub 4}){sub 2}, containing a long Au-Cu distance of {approx}4.72 {angstrom} is formed. Additionally, as the byproduct of the reaction of CuBr with [Au(CH{sub 3}imCH{sub 2}quin){sub 2}]BF{sub 4} the deep-red, dimetallic compound, AuCuBr{sub 2}(CH{sub 3}imCH{sub 2}quin){sub 2}, was isolated in very low yield. All of these complexes were studied by NMR spectroscopy, mass spectrometry, and the copper containing species were additionally characterized by X-ray crystallography. In solution the copper centers dissociate from the gold complexes, but as shown by XANES and EXAFS spectroscopy, at low temperature the Cu-Cu linkage is broken, and the individual copper(I) halides reposition themselves to opposite sides of the gold complex while remaining coordinated to one imine moiety. In the solid state all of the complexes are photoluminescent, though the nature of the excited state was not determined.« less

Warming Early Mars With CH4

NASA Astrophysics Data System (ADS)

Justh, H. L.; Kasting, J. F.

2002-12-01

ratios will be presented. This use of climate modeling is important since it is the fundamental way that the magnitude of possible geochemical and biological CH4 sources can be related to predicted CH4 concentrations in the early martian atmosphere. References: 1) Gough, D. O. Solar Physics 74, 21-34 (1981). 2) Carr, M. H. Water on Mars (1996). 3) Kasting, J. F. Icarus 94, 1-13 (1991). 4) Forget, F., and Pierrehumbert R. T. Science 278, 1273-1276 (1997). 5) Mischna, M. A., Kasting J. F., Pavlov A., and Freedman R. Icarus 145, 546-554 (2000).

CH-53K Heavy Lift Replacement Helicopter (CH-53K)

DTIC Science & Technology

2015-12-01

Selected Acquisition Report (SAR) RCS: DD-A&T(Q&A)823-390 CH-53K Heavy Lift Replacement Helicopter (CH-53K) As of FY 2017 President’s Budget...December 2015 SAR March 4, 2016 10:04:18 UNCLASSIFIED 4 Col Henry Vanderborght PMA-261 Heavy Lift Helicopters Program Executive Office - Air, Anti...Replacement Helicopter (CH-53K) DoD Component Navy Responsible Office References SAR Baseline (Development Estimate) Defense Acquisition Executive (DAE

Dynamics of the F(-) + CH3I → HF + CH2I(-) Proton Transfer Reaction.

PubMed

Zhang, Jiaxu; Xie, Jing; Hase, William L

2015-12-17

Direct chemical dynamics simulations, at collision energies Erel of 0.32 and 1.53 eV, were performed to obtain an atomistic understanding of the F(-) + CH3I reaction dynamics. There is only the F(-) + CH3I → CH3F + I(-) bimolecular nucleophilic substitution SN2 product channel at 0.32 eV. Increasing Erel to 1.53 eV opens the endothermic F(-) + CH3I → HF + CH2I(-) proton transfer reaction, which is less competitive than the SN2 reaction. The simulations reveal proton transfer occurs by two direct atomic-level mechanisms, rebound and stripping, and indirect mechanisms, involving formation of the F(-)···HCH2I complex and the roundabout. For the indirect trajectories all of the CH2I(-) is formed with zero-point energy (ZPE), while for the direct trajectories 50% form CH2I(-) without ZPE. Without a ZPE constraint for CH2I(-), the reaction cross sections for the rebound, stripping, and indirect mechanisms are 0.2 ± 0.1, 1.2 ± 0.4, and 0.7 ± 0.2 Å(2), respectively. Discarding trajectories that do not form CH2I(-) with ZPE reduces the rebound and stripping cross sections to 0.1 ± 0.1 and 0.7 ± 0.5 Å(2). The HF product is formed rotationally and vibrationally unexcited. The average value of J is 2.6 and with histogram binning n = 0. CH2I(-) is formed rotationally excited. The partitioning between CH2I(-) vibration and HF + CH2I(-) relative translation energy depends on the treatment of CH2I(-) ZPE. Without a CH2I(-) ZPE constraint the energy partitioning is primarily to relative translation with little CH2I(-) vibration. With a ZPE constraint, energy partitioning to CH2I(-) rotation, CH2I(-) vibration, and relative translation are statistically the same. The overall F(-) + CH3I rate constant at Erel of both 0.32 and 1.53 eV is in good agreement with experiment and negligibly affected by the treatment of CH2I(-) ZPE, since the SN2 reaction is the major contributor to the total reaction rate constant. The potential energy surface and reaction dynamics for F

Capture and dissociation in the complex-forming CH + H2 → CH2 + H, CH + H2 reactions.

PubMed

González, Miguel; Saracibar, Amaia; Garcia, Ernesto

2011-02-28

The rate coefficients for the capture process CH + H(2)→ CH(3) and the reactions CH + H(2)→ CH(2) + H (abstraction), CH + H(2) (exchange) have been calculated in the 200-800 K temperature range, using the quasiclassical trajectory (QCT) method and the most recent global potential energy surface. The reactions, which are of interest in combustion and in astrochemistry, proceed via the formation of long-lived CH(3) collision complexes, and the three H atoms become equivalent. QCT rate coefficients for capture are in quite good agreement with experiments. However, an important zero point energy (ZPE) leakage problem occurs in the QCT calculations for the abstraction, exchange and inelastic exit channels. To account for this issue, a pragmatic but accurate approach has been applied, leading to a good agreement with experimental abstraction rate coefficients. Exchange rate coefficients have also been calculated using this approach. Finally, calculations employing QCT capture/phase space theory (PST) models have been carried out, leading to similar values for the abstraction rate coefficients as the QCT and previous quantum mechanical capture/PST methods. This suggests that QCT capture/PST models are a good alternative to the QCT method for this and similar systems.

Inhibition of Serratia marcescens Smj-11 biofilm formation by Alcaligenes faecalis STN17 crude extract

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

Lutfi, Zainal; Ahmad, Asmat; Usup, Gires

Serratia marcescens biofilms are formed when they are bound to surfaces in aqueous environments. S. marcescens utilizes N-acylhomoserine lactone (AHL) as its quorum sensing signal molecule. The accumulation of AHL indicates the bacteria to produce matrices to form biofilms. Prodigiosin (2-methyl-3-pentyl-6-methoxyprodigiosin), which causes red pigmentation in the colonies, are also produced when the AHL reaches a certain threshold. The Alcaligenes faecalis STN17 crude extract is believed to inhibit quorum sensing in the S. marcescens Smj-11 and, thus, impedes its biofilm formation ability. A. faecalis STN17 was grown in marine broth, and ethyl acetate extraction was carried out. The crude compoundmore » of A. faecalis STN17 was diluted at high concentration (0.2-6.4 mg/mL) and was taken to confirm anti-biofilm activity through the crystal violet method in 96-wells plate. Then, the crude extract underwent purification using simple solvents partitioning test to discern the respective compounds that had the anti-biofilm activity under the crystal violet method. The crystal violet test showed that the crude did have anti-biofilm activity on S. marcescens Smj-11, but did not kill the cells. This finding signifies that the suppression of biofilm formation in S. marcescens by A. faecalis STN17 has a strong correlation. The partitioning test showed that A. faecalis STN17 crude extract has several compounds and only the compound(s) in chloroform showed activities. In conclusion, the crude extract of A. faecalis STN17 has the ability to inhibit S. marcescens Smj-11 biofilm formation.« less

Conformational and spectroscopic study of xanthogen ethyl formates, ROC(S)SC(O)OCH2CH3. Isolation of CH3CH2OC(O)SH

NASA Astrophysics Data System (ADS)

Juncal, Luciana C.; Cozzarín, Melina V.; Romano, Rosana M.

2015-03-01

ROC(S)SC(O)OCH2CH3, with R = CH3sbnd , (CH3)2CHsbnd and CH3(CH2)2sbnd , were obtained through the reaction between potassium xanthate salts, ROC(S)SK, and ethyl chloroformate, ClC(O)OCH2CH3. The liquid compounds were identified and characterized by 1H and 13C NMR and mass spectrometry. The conformations adopted by the molecules were studied by DFT methods. 6 conformers were theoretically predicted for R = CH3sbnd and (CH3)2CHsbnd , while the conformational flexibility of the n-propyl substituent increases the total number of feasible rotamers to 21. For the three molecules, the conformers can be associated in 3 groups, being the most stable the AS forms - the Cdbnd S double bond anti (A) with respect to the Csbnd S single bond and the Ssbnd C single bond syn (S) with respect to the Cdbnd O double bond - followed by AA and SS conformers. The vibrational spectra were interpreted in terms of the predicted conformational equilibrium, presenting the ν(Cdbnd O) spectral region signals corresponding to the three groups of conformers. A moderated pre-resonance Raman enhancement of the ν(Cdbnd S) vibrational mode of CH3(CH2)2OC(S)SC(O)OCH2CH3 was detected, when the excitation radiation approaches the energy of a n → π∗ electronic transition associated with the Cdbnd S chromophore. UV-visible spectra in different solvents were measured and interpreted in terms of TD-DFT calculations. The unknown molecule CH3CH2OC(O)SH was isolated by the UV-visible photolysis of CH3OC(S)SC(O)OCH2CH3 isolated in Ar matrix, and also obtained as a side-product of the reaction between potassium xanthate salts, ROC(S)SK, and ethyl chloroformate, ClC(O)OCH2CH3.

Thermal decomposition of ethanol. 4. Ab initio chemical kinetics for reactions of H atoms with CH3CH2O and CH3CHOH radicals.

PubMed

Xu, Z F; Xu, Kun; Lin, M C

2011-04-21

The potential energy surfaces of H-atom reactions with CH(3)CH(2)O and CH(3)CHOH, two major radicals in the decomposition and oxidation of ethanol, have been studied at the CCSD(T)/6-311+G(3df,2p) level of theory with geometric optimization carried out at the BH&HLYP/6-311+G(3df,2p) level. The direct hydrogen abstraction channels and the indirect association/decomposition channels from the chemically activated ethanol molecule have been considered for both reactions. The rate constants for both reactions have been calculated at 100-3000 K and 10(-4) Torr to 10(3) atm Ar pressure by microcanonical VTST/RRKM theory with master equation solution for all accessible product channels. The results show that the major product channel of the CH(3)CH(2)O + H reaction is CH(3) + CH(2)OH under atmospheric pressure conditions. Only at high pressure and low temperature, the rate constant for CH(3)CH(2)OH formation by collisonal deactivation becomes dominant. For CH(3)CHOH + H, there are three major product channels; at high temperatures, CH(3)+CH(2)OH production predominates at low pressures (P < 100 Torr), while the formation of CH(3)CH(2)OH by collisional deactivation becomes competitive at high pressures and low temperatures (T < 500 K). At high temperatures, the direct hydrogen abstraction reaction producing CH(2)CHOH + H(2) becomes dominant. Rate constants for all accessible product channels in both systems have been predicted and tabulated for modeling applications. The predicted value for CH(3)CHOH + H at 295 K and 1 Torr pressure agrees closely with available experimental data. For practical modeling applications, the rate constants for the thermal unimolecular decomposition of ethanol giving key accessible products have been predicted; those for the two major product channels taking place by dehydration and C-C breaking agree closely with available literature data.

Ab Initio Chemical Kinetics for the CH3 + O((3)P) Reaction and Related Isomerization-Decomposition of CH3O and CH2OH Radicals.

PubMed

Xu, Z F; Raghunath, P; Lin, M C

2015-07-16

The kinetics and mechanism of the CH3 + O reaction and related isomerization-decomposition of CH3O and CH2OH radicals have been studied by ab initio molecular orbital theory based on the CCSD(T)/aug-cc-pVTZ//CCSD/aug-cc-pVTZ, CCSD/aug-cc-pVDZ, and G2M//B3LYP/6-311+G(3df,2p) levels of theory. The predicted potential energy surface of the CH3 + O reaction shows that the CHO + H2 products can be directly generated from CH3O by the TS3 → LM1 → TS7 → LM2 → TS4 path, in which both LM1 and LM2 are very loose and TS7 is roaming-like. The result for the CH2O + H reaction shows that there are three low-energy barrier processes including CH2O + H → CHO + H2 via H-abstraction and CH2O + H → CH2OH and CH2O + H → CH3O by addition reactions. The predicted enthalpies of formation of the CH2OH and CH3O radicals at 0 K are in good agreement with available experimental data. Furthermore, the rate constants for the forward and some key reverse reactions have been predicted at 200-3000 K under various pressures. Based on the new reaction pathway for CH3 + O, the rate constants for the CH2O + H and CHO + H2 reactions were predicted with the microcanonical variational transition-state/Rice-Ramsperger-Kassel-Marcus (VTST/RRKM) theory. The predicted total and individual product branching ratios (i.e., CO versus CH2O) are in good agreement with experimental data. The rate constant for the hydrogen abstraction reaction of CH2O + H has been calculated by the canonical variational transition-state theory with quantum tunneling and small-curvature corrections to be k(CH2O + H → CHO + H2) = 2.28 × 10(-19) T(2.65) exp(-766.5/T) cm(3) molecule(-1) s(-1) for the 200-3000 K temperature range. The rate constants for the addition giving CH3O and CH2OH and the decomposition of the two radicals have been calculated by the microcanonical RRKM theory with the time-dependent master equation solution of the multiple quantum well system in the 200-3000 K temperature range at 1 Torr to

Electron spin resonance of (CO 2 H)CH 2 CH 2 CH(CO 2 H) in irradiated glutaric acid

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

Horsfield, A.; Morton, J. R.; Whiffen, D. H.

It is concluded from electron spin resonance spectra that the radical (CO 2 H)CH 2 CH 2 CH(CO 2 H) remains trapped in a glutaric acid crystal after gamma -irradiation. This radical is found in two different conformations. Approximate hyperfine coupling constants are given for each, although exact interpretation is hindered by the overlapping of spectra. Reasons for the formation of the two forms of the radical are discussed.

Metabolic pathway engineering in cotton: Biosynthesis of polyhydroxybutyrate in fiber cells

PubMed Central

John, Maliyakal E.; Keller, Greg

1996-01-01

Alcaligenes eutrophus genes encoding the enzymes, β-ketothiolase (phaA), acetoacetyl-CoA reductase (phaB), and polyhydroxyalkanoate synthase (phaC) catalyze the production of aliphatic polyester poly-d-(−)-3-hydroxybutyrate (PHB) from acetyl-CoA. PHB is a thermoplastic polymer that may modify fiber properties when synthesized in cotton. Endogenous β-ketothiolase activity is present in cotton fibers. Hence cotton was transformed with engineered phaB and phaC genes by particle bombardment, and transgenic plants were selected based on marker gene, β-glucuronidase (GUS), expression. Fibers of 10 transgenic plants expressed phaB gene, while eight plants expressed both phaB and phaC genes. Electron microscopy examination of fibers expressing both genes indicated the presence of electron-lucent granules in the cytoplasm. High pressure liquid chromatography, gas chromatography, and mass spectrometry evidence suggested that the new polymer produced in transgenic fibers is PHB. Sixty-six percent of the PHB in fibers is in the molecular mass range of 0.6 × 106 to 1.8 × 106 Da. The presence of PHB granules in transgenic fibers resulted in measurable changes of thermal properties. The fibers exhibited better insulating characteristics. The rate of heat uptake and cooling was slower in transgenic fibers, resulting in higher heat capacity. These data show that metabolic pathway engineering in cotton may enhance fiber properties by incorporating new traits from other genetic sources. This is an important step toward producing new generation fibers for the textile industry. PMID:11038522

Rate Constants for the Reactions of OH with CH(sub 3)Cl, CH(sub 2) C1(sub 2), CHC1(sub 3)and CH(sub 3)Br

NASA Technical Reports Server (NTRS)

Hsu, H-J.; DeMore, W.

1994-01-01

Rate constants for the reactions of OH with CH3C1, CH2Cl2, CHCl3 and CH3Br have been measured by a relative rate technique in which the reaction rate of each compound was compared to that of HFC-152a (CH3CHF2)and for CH2Cl2, HFC-161 (CH3CH2F).

Low-Temperature Hydrocarbon Photochemistry: CH3 + CH3 Recombination in Giant Planet Atmospheres

NASA Technical Reports Server (NTRS)

Smith, Gregory P.; Huestis, David L.

2002-01-01

Planetary emissions of the methyl radical CH3 were observed for the first time in 1998 on Saturn and Neptune by the ISO (Infrared Space Observatory) mission satellite. CH3 is produced by VUV photolysis of CH4 and is the key photochemical intermediate leading complex organic molecules on the giant planets and moons. The CH3 emissions from Saturn were unexpectedly weak. A suggested remedy is to increase the rate of the recombination reaction CH3 + CH3 + H2 --> C2H6 + H2 at 140 K to a value at least 10 times that measured at room temperature in rare gases, but within the range of disagreeing theoretical expressions at low temperature. We are performing laboratory experiments at low temperature and very low pressure. The experiments are supported by RRKM theoretical modeling that is calibrated using the extensive combustion literature.

Unusual reaction paths of SN2 nucleophile substitution reactions CH4 + H- → CH4 + H- and CH4 + F- → CH3F + H-: Quantum chemical calculations

NASA Astrophysics Data System (ADS)

Minyaev, Ruslan M.; Quapp, Wolfgang; Schmidt, Benjamin; Getmanskii, Ilya V.; Koval, Vitaliy V.

2013-11-01

Quantum chemical (CCSD(full)/6-311++G(3df,3pd), CCSD(T)(full)/6-311++G(3df,3pd)) and density function theory (B3LYP/6-311++G(3df,3pd)) calculations were performed for the SN2 nucleophile substitution reactions CH4 + H- → CH4 + H- and CH4 + F- → CH3F + H-. The calculated gradient reaction pathways for both reactions have an unusual behavior. An unusual stationary point of index 2 lies on the gradient reaction path. Using Newton trajectories for the reaction path, we can detect VRI point at which the reaction path branches.

Reflected shock tube studies of high-temperature rate constants for OH + CH4 --> CH3 + H2O and CH3 + NO2 --> CH3O + NO.

PubMed

Srinivasan, N K; Su, M-C; Sutherland, J W; Michael, J V

2005-03-10

The reflected shock tube technique with multipass absorption spectrometric detection of OH radicals at 308 nm has been used to study the reactions OH + CH(4) --> CH(3) + H(2)O and CH(3) + NO(2) --> CH(3)O + NO. Over the temperature range 840-2025 K, the rate constants for the first reaction can be represented by the Arrhenius expression k = (9.52 +/- 1.62) x 10(-11) exp[(-4134 +/- 222 K)/T] cm(3) molecule(-1) s(-1). Since this reaction is important in both combustion and atmospheric chemistry, there have been many prior investigations with a variety of techniques. The present results extend the temperature range by 500 K and have been combined with the most accurate earlier studies to derive an evaluation over the extended temperature range 195-2025 K. A three-parameter expression describes the rate behavior over this temperature range, k = (1.66 x 10(-18))T(2.182) exp[(-1231 K)/T] cm(3) molecule(-1) s(-1). Previous theoretical studies are discussed, and the present evaluation is compared to earlier theoretical estimates. Since CH(3) radicals are a product of the reaction and could cause secondary perturbations in rate constant determinations, the second reaction was studied by OH radical production from the fast reactions CH(3)O --> CH(2)O + H and H + NO(2) --> OH + NO. The measured rate constant is 2.26 x 10(-11) cm(3) molecule(-1) s(-1) and is not dependent on temperature from 233 to 1700 K within experimental error.

Total cross sections of electron scattering by molecules NF3, PF3, N(CH3)3, P(CH3)3, NH(CH3)2, PH(CH3)2, NH2CH3 and PH2CH3 at 30-5000 eV

NASA Astrophysics Data System (ADS)

Shi, D. H.; Sun, J. F.; Zhu, Z. L.; Liu, Y. F.

2010-04-01

Total cross sections of electron scattering by eight molecules NF3, PF3, N(CH3)3, P(CH3)3, NH(CH3)2, PH(CH3)2, NH2CH3 and PH2CH3, which have some structural similarities, are calculated at the Hartree-Fork level by the modified additivity rule approach [D.H. Shi, J.F. Sun, Z.L. Zhu, H. Ma, Y.F. Liu, Eur. Phys. J. D 45, 253 (2007); D.H. Shi, J.F. Sun, Y.F. Liu, Z.L. Zhu, X.D. Yang, Chin. Opt. Lett. 4, 192 (2006)]. The modified additivity rule approach takes into considerations that the contributions of the geometric shielding effect vary as the energy of incident electrons, the dimension of target molecule, the number of electrons in the molecule and the number of atoms constituting the molecule. The present investigations cover the impact energy range from 30 to 5000 eV. The quantitative total cross sections are compared with those obtained by experiments and other theories. Excellent agreement is observed even at energies of several tens of eV. It shows that the modified additivity rule approach is applicable to carry out the total cross section calculations of electron scattering by these molecules at intermediate and high energies, in particular over the energy range above 80 eV or so. It proves that the microscopic molecular properties, such as the geometrical size of the target and the number of atoms constituting the molecule, are of crucial importance in the TCS calculations. The new results for PH(CH3)2 and PH2CH3 are also presented at energies from 30 to 5000 eV, although no experimental and theoretical data are available for comparison. In the present calculations, the atoms are still represented by the spherical complex optical potential, which is composed of static, exchange, polarization and absorption terms.

Two-wavelength single laser CH and CH(4) imaging in a lifted turbulent diffusion flame.

PubMed

Namazian, M; Schmitt, R L; Long, M B

1988-09-01

A new technique has been developed which allows simultaneous 2-D mapping of CH and CH 4 in a turbulent methane flame. A flashlamp-pumped dye laser using two back mirrors produces output at 431.5 and 444 nm simultaneously. The 431.5-nm line is used to excite the (0, 0) band of the A(2)Delta-X(2)Pi system of CH, and the fluorescence of the (0, 1) transition is observed at 489 nm. Coincidentally, the spontaneous Raman scattering from CH(4) also occurs near 489 nm for a 431.5-nm excitation. To separate the CH(4) and CH contributions, the 444-nm line is used to produce a spontaneous Raman signal from CH(4) that is spectrally separated from the CH fluorescence. Subtraction of the signals generated by the 431.5- and 444-nm wavelength beams yields separate measurements of CH(4) and CH. Raman-scattered light records the instantaneous distribution of the fuel, and simultaneously the CH fluorescence indicates the location of the flame zone. The resulting composite images provide important insight on the interrelationship between fuel-air mixing and subsequent combustion.M. Namazian is with Altex Technologies Corporation, 109 Via De Tesoros, Los Gatos, California 95030; R. L. Schmitt is with Sandia National Laboratories, Combustion Research Facility, Livermore, California 94550; and M. B. Long is with Yale University, Department of Mechanical Engineering, New Haven, Connecticut 06520.

Electron driven processes in sulphur containing compounds CH3SCH3 and CH3SSCH3

NASA Astrophysics Data System (ADS)

Kopyra, Janina; Władziński, Jakub

2015-06-01

Dissociative electron attachment to gas phase dimethyl sulphide (CH3SCH3) and dimethyl disulphide (CH3SSCH3) has been studied by means of a crossed beams apparatus. Cleavage of the C-S bond within CH3SCH3 and the S-S bond within CH3SSCH3 is observed within a resonance in the energy range below 2 eV and visible preferentially via the appearance of the fragment CH2S-. The striking finding is that the intensity of CH2S- generated from CH3SSCH3 is more than two orders of magnitude higher than the intensity of the respective anionic fragment generated from CH3SCH3. Our results clearly demonstrate that the CH3SSCH3 molecule, which contains disulphide bridge is substantially more sensitive towards electron attachment resulting mainly in dissociation along the S-S bridge.

Scaled Hartree-Fock force field calculations for organothallium compounds: Normal-mode analysis for TlCH sub 3 Tl(CH sub 3 ) sub 2 sup + , Tl(CH sub 3 ) sub 3 , Tl(CH sub 3 ) sub 2 Br, and Tl(CH sub 3 ) sub 4 sup minus

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

Schwerdtfeger, P.; Bowmaker, G.A.; Boyd, P.D.W.

1990-02-01

In a recent paper we presented Hartree-Fock (HF) calculations for aliphatic organothallium compounds. The diagonal HF force constants obtained from a Fletcher-Powell geometry optimization are now used for a normal-mode analysis of TlCH{sub 3}, Tl(CH{sub 3}){sub 2}{sup +}, Tl(CH{sub 3}){sub 3}, Tl(CH{sub 3}){sub 2}Br, and Tl(CH{sub 3}){sub 4}{sup {minus}}. In order to calculate frequencies comparable to experimental values, the HF force field has been scaled by using scaling factors obtained from experimental infrared and Raman measurements on Tl(CH{sub 3}){sub 2}{sup +} and TlBr. The vibrational spectra of Tl(CH{sub 3}){sub 2}{sup +} were remeasured (infrared and Raman) in order to obtainmore » an accurate force field. Predictions are made for the vibrational spectrum of the as yet undetected TlCH{sub 3} molecule. Experimental infrared and Raman results for Tl(CH{sub 3}){sub 3} compare reasonably well with our calculated frequencies. Relativistic and correlation effects are analyzed for the vibrational frequencies of Tl(CH{sub 3}){sub 2}{sup +}.« less

Optical emission spectroscopic studies and comparisons of CH{sub 3}F/CO{sub 2} and CH{sub 3}F/O{sub 2} inductively coupled plasmas

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

Lou, Qiaowei; Kaler, Sanbir; Donnelly, Vincent M., E-mail: vmdonnelly@uh.edu

2015-03-15

A CH{sub 3}F/CO{sub 2} inductively coupled plasma (ICP), sustained in a compact plasma reactor, was investigated as a function of power (5–400 W) and feed gas composition, at a pressure of 10 mTorr, using optical emission spectroscopy and rare gas actinometry. Number densities of H, F, and O increased rapidly between 74% and 80% CO{sub 2}, ascribed to the transition from polymer-covered to polymer-free reactor walls, similar to that found previously in CH{sub 3}F/O{sub 2} ICPs at 48% O{sub 2}. Below 40% O{sub 2} or CO{sub 2}, relative emission intensity ratios were almost identical for most key species in CH{sub 3}F/O{submore » 2} and CH{sub 3}F/CO{sub 2} ICPs except for higher OH/Xe (a qualitative measure of OH and H{sub 2}O densities) over the full range of CH{sub 3}F/O{sub 2} composition. The number density of H, F, and O increased with power in CH{sub 3}F/CO{sub 2} (20%/80%) plasmas (polymer-free walls), reaching 4.0, 0.34, and 1.6 × 10{sup 13}/cm{sup 3}, respectively, at 300 W. The CO number density increased with power and was estimated, based on self-actinometry, to be 8.8 × 10{sup 13}/cm{sup 3} at 300 W. The CO{sub 2} number density was independent of power below 40 W (where very little decomposition occurred), and then decreased rapidly with increasing power, reaching 2.8 × 10{sup 13}/cm{sup 3} at 300 W, corresponding to 83% dissociation. Films deposited on p-Si, 10 cm from the open, downstream end of the plasma reactor, were analyzed by x-ray photoelectron spectroscopy. Between 10% and 40% CO{sub 2} or O{sub 2} addition to CH{sub 3}F, film deposition rates fell and O content in the films increased. Faster deposition rates in CH{sub 3}F/CO{sub 2} plasmas were ascribed mainly to a larger thermodynamic driving force to form solid carbon, compared with CH{sub 3}F/O{sub 2} plasmas. Oxygen content in the films increased with increasing CO{sub 2} or O{sub 2} addition, but for the same deposition rate, no substantial differences

Formation of unexpected silicon- and disiloxane-bridged multiferrocenyl derivatives bearing Si-O-CH[double bond, length as m-dash]CH2 and Si-(CH2)2C(CH3)3 substituents via cleavage of tetrahydrofuran and trapping of its ring fragments.

PubMed

Bruña, Sonia; González-Vadillo, Ana Mª; Ferrández, Marta; Perles, Josefina; Montero-Campillo, M Merced; Mó, Otilia; Cuadrado, Isabel

2017-09-12

The formation of a family of silicon- and siloxane-bridged multiferrocenyl derivatives carrying different functional groups attached to silicon, including Fc 2 (CH 3 ) 3 C(CH 2 ) 2 SiCH[double bond, length as m-dash]CH 2 (5), Fc 2 (CH 2 [double bond, length as m-dash]CH-O)SiCH[double bond, length as m-dash]CH 2 (6), Fc 2 (OH)SiCH[double bond, length as m-dash]CH 2 (7), Fc 2 (CH 2 [double bond, length as m-dash]CH-O)Si-O-Si(O-CH[double bond, length as m-dash]CH 2 )Fc 2 (8) and Fc 2 (CH 2 [double bond, length as m-dash]CH-O)Si-O-SiFc 3 (9) is described. Silyl vinyl ether molecules 6, 8 and 9 and the heteroleptic vinylsilane 5 resulted from the competing metathesis reaction of lithioferrocene (FcLi), CH 2 [double bond, length as m-dash]CH-OLi or (CH 3 ) 3 C(CH 2 ) 2 Li with the corresponding multifunctional chlorosilane, Cl 3 SiCH[double bond, length as m-dash]CH 2 or Cl 3 Si-O-SiCl 3 . The last two organolithium species have been likely formed in situ by fragmentation of the tetrahydrofuran solvent. Diferrocenylvinyloxyvinylsilane 6 is noteworthy since it represents a rare example of a redox-active silyl mononomer in which two different C[double bond, length as m-dash]C polymerisable groups are directly connected to silicon. The molecular structures of the silicon-containing multiferrocenyl species 5, 6, 8 and 9 have been investigated by single-crystal X-ray diffraction studies, demonstrating the capture and storage processes of two ring fragments resulting from the cleavage of cyclic THF in redox-active and stable crystalline organometallic compounds. From electrochemical studies we found that by changing the anion of the supporting electrolyte from [PF 6 ] - to [B(C 6 F 5 ) 4 ] - , the redox behaviour of tetrametallic disiloxane 8 can be switched from a poorly resolved multistep redox process to four consecutive well-separated one-electron oxidations, corresponding to the sequential oxidation of the four ferrocenyl moieties.

The effect of water regime and soil management on methane (CH4) emission of rice field

NASA Astrophysics Data System (ADS)

Naharia, O.; Setyanto, P.; Arsyad, M.; Burhan, H.; Aswad, M.

2018-05-01

Mitigation of CH4 emission of rice field is becoming a serious issue. The Agricultural Environment Preservation Research Station in Central Java conducted a field study to investigate the effect of water regime and soil tillage on CH4 emission from paddy fields. Treatments consisted of two factors. The first factor was water regime, e.g., 1) continuously flooded 5 cm, 2) intermittent irrigation and 3) saturated water condition at 0-1 cm water level. The second factor was soil management, e.g., 1) normal tillage, 2) zero tillage + 3 sulfosate ha-1 and 3) zero tillage + 3 L paraquat ha-1. Most of treatments gave a significant reduction of total CH4 emission between 34 – 85% during the wet season crop as compared to normal rice cropping practice, while in the dry season the CH4 reduction ranged between 16 – 92%. No-tillage with non-selective herbicides combined with intermittent/saturated irrigation system significantly reduced methane emission without significantly affecting rice productivity as compared to normal tillage with continuous flooding (farmers practice)

Reclassification of Alcaligenes latus strains IAM 12599T and IAM 12664 and Pseudomonas saccharophila as Azohydromonas lata gen. nov., comb. nov., Azohydromonas australica sp. nov. and Pelomonas saccharophila gen. nov., comb. nov., respectively.

PubMed

Xie, Cheng-Hui; Yokota, Akira

2005-11-01

The aim of this study was to clarify the taxonomic position of the nitrogen-fixing and hydrogen-oxidizing bacteria Alcaligenes latus strains IAM 12599T, IAM 12664 and IAM 12665 and Pseudomonas saccharophila IAM 14368T. It was found that the type strain of Alcaligenes latus, IAM 12599T, showed 99 x 9 and 96 x 1 % 16S rRNA gene sequence similarity to strains IAM 12665 and IAM 12664, respectively. A comparison using DNA-DNA hybridization suggested that strains IAM 12599T and IAM 12665 belong to a single species (89 x 7 %) and that strain IAM 12664 (35 x 1 %) forms a separate species. The phenotypic characteristics also support the conclusion that these bacteria should be identified as two species of a new genus: Azohydromonas lata gen. nov., comb. nov. (type strain IAM 12599T=DSM 1122T=LMG 3321T=ATCC 29712T; reference strain IAM 12665=DSM 1123=LMG 3325=ATCC 29714) and Azohydromonas australica sp. nov. (type strain IAM 12664T=DSM 1124T=LMG 3324T=ATCC 29713T). Pseudomonas saccharophila IAM 14368T was found to be closely related to the phototrophic bacterium Roseateles depolymerans, with 96 x 8 % 16S rRNA gene sequence similarity, but the two bacteria are quite different with respect to their metabolism and some significant phenotypic characteristics, suggesting that they cannot be included in a single genus. Further studies on their nifH gene sequences, G+C content of the DNA and cellular fatty acid composition confirm that Pseudomonas saccharophila should be reclassified: the name Pelomonas saccharophila gen. nov., comb. nov. is proposed, with the type strain IAM 14368T (=LMG 2256T=ATCC 15946T).

Direct observation of unimolecular decay of CH 3 CH 2 CHOO Criegee intermediates to OH radical products

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

Fang, Yi; Liu, Fang; Klippenstein, Stephen J.

2016-07-28

The unimolecular decay of carbonyl oxide intermediates, known as Criegee intermediates, produced in alkene ozonolysis is a significant source of OH radicals in the troposphere. Here, the rate of appearance of OH radical products is examined directly in the time-domain for a prototypical alkyl-substituted Criegee intermediate, CH3CH2CHOO, following vibrational activation under collision-free conditions. Complementary statistical Rice-Ramsperger-Kassel-Marcus calculations of the microcanonical unimolecular decay rate for CH3CH2CHOO are also carried out at energies in the vicinity of the barrier for 1,4 hydrogen atom transfer that leads to OH products. Tunneling through the barrier, derived from high level electronic structure calculations, contributes significantlymore » to the decay rate. Infrared transitions of CH3CH2CHOO are identified in the CH stretch overtone region, which are detected by ultraviolet laser-induced fluorescence of the resultant OH products. The features observed are attributed to CH vibrational excitations and conformational forms utilizing insights from theory. Both experiment and theory yield unimolecular decay rates for CH3CH2CHOO of ca. 10(7) s(-1), which are slower than those obtained for syn-CH3CHOO or (CH3)(2)COO reported previously [Fang et al., J. Chem. Phys. 144, 061102 (2016)] at similar energies. Master equation modeling is also utilized to predict the thermal decay rate of CH3CH2CHOO under atmospheric conditions, giving a rate of 279 s(-1) at 298 K.« less

Experimental and theoretical study of the gas phase reaction of ethynyl radical with methane (HCC+CH 4)

NASA Astrophysics Data System (ADS)

Ceursters, Benny; Thi Nguyen, Hue Minh; Peeters, Jozef; Tho Nguyen, Minh

2000-10-01

Absolute rate coefficients of the reaction of ethynyl radical with methane were measured for the first time at higher temperatures by a pulsed laser photolysis/chemiluminescence (PLP/CL) technique. Ethynyl radicals (HCC) radicals were generated pulsewise upon excimer laser photodissociation of acetylene at 193 nm and pseudo-first-order exponential decays of thermalized HCC were monitored in real-time by the CH( A2Δ → X2Π ) chemiluminescence produced by their reaction with O 2. The rate coefficients k(HCC+CH 4), over 295⩽T ( K)<800 , exhibit strong non-Arrhenius behaviour, being k(T)=1.39×10 -18T 2.34±0.40exp[(380±180) K/T] cm3 molecule-1 s-1. Calculations at the CCSD(T)/aug-cc-pvTZ level reveal that the direct H-abstraction yielding HCCH+CH 3 has the lowest energy barrier of about 10 kJ mol -1.

Nuclear Hyperfine Structure in the Donor – Acceptor Complexes (CH3)3N-BF3 and (CH)33N-B(CH3)3

EPA Science Inventory

The donor-acceptor complexes (CH3)3N-BF3 and (CH3)3N-B(CH3)3 have been reinvestigated at high resolution by rotational spectroscopy in a supersonic jet. Nuclear hyperfine structure resulting from both nitrogen and boron has been resolved and quadrupole coupling constants have bee...

Organophosphate and carbamate insecticides in agricultural waters and cholinesterase (ChE) inhibition in common carp (Cyprinus carpio)

USGS Publications Warehouse

Gruber, S.J.; Munn, M.D.

1998-01-01

Cholinesterase (ChE) activity was used as a biomarker for assessing exposure of common carp (Cyprinus carpio) to organophosphate and carbamate insecticides from irrigated agricultural waters. Carp were collected from a lake (Royal Lake) that receives most of its water from irrigation return flows and from a reference lake (Billy Clapp Lake) outside of the irrigation system. Results indicated that the mean whole-brain ChE activity of carp from Royal Lake (3.47 μmol/min/g tissue) was 34.2% less than that of carp from Billy Clapp Lake (5.27 μmol/min/g tissue) (p = 0.003). The depressed ChE activity in brain tissue of Royal Lake carp was in response to ChE-inhibiting insecticides detected in water samples in the weeks prior to tissue sampling; the most frequently detected insecticides included chlorpyrifos, azinphos-methyl, carbaryl, and ethoprop. Neither sex nor size appears to be a covariable in the analysis; ChE activity was not correlated with fish length or weight in either lake and there was no significant difference in ChE activity between the two sexes within each lake. Although organophosphate and carbamate insecticides can break down rapidly in the environment, this study suggests that in agricultural regions where insecticides are applied for extended periods of the year, nontarget aquatic biota may be exposed to high levels of ChE-inhibiting insecticides for a period of several months.

Binary properties of CH and carbon-enhanced metal-poor stars

NASA Astrophysics Data System (ADS)

Jorissen, A.; Van Eck, S.; Van Winckel, H.; Merle, T.; Boffin, H. M. J.; Andersen, J.; Nordström, B.; Udry, S.; Masseron, T.; Lenaerts, L.; Waelkens, C.

2016-02-01

The HERMES spectrograph installed on the 1.2-m Mercator telescope has been used to monitor the radial velocity of 13 low-metallicity carbon stars, among which seven carbon-enhanced metal-poor (CEMP) stars and six CH stars (including HIP 53522, a new member of the family, as revealed by a detailed abundance study). All stars but one show clear evidence for binarity. New orbits are obtained for eight systems. The sample covers an extended range in orbital periods, extending from 3.4 d (for the dwarf carbon star HE 0024-2523) to about 54 yr (for the CH star HD 26, the longest known among barium, CH, and extrinsic S stars). Three systems exhibit low-amplitude velocity variations with periods close to 1 yr superimposed on a long-term trend. In the absence of an accurate photometric monitoring of these systems, it is not clear yet whether these variations are the signature of a very low-mass companion or of regular envelope pulsations. The period - eccentricity (P - e) diagram for the 40 low-metallicity carbon stars with orbits now available shows no difference between CH and CEMP-s stars (the latter corresponding to those CEMP stars enriched in s-process elements, as are CH stars). We suggest that they must be considered as one and the same family and that their different names only stem from historical reasons. Indeed, these two families have as well very similar mass-function distributions, corresponding to companions with masses in the range 0.5-0.7 M⊙, indicative of white-dwarf companions, adopting 0.8-0.9 M⊙ for the primary component. This result confirms that CH and CEMP-s stars obey the same mass-transfer scenario as their higher-metallicity analogues, barium stars. The P - e diagrams of barium, CH, and CEMP-s stars are indeed very similar. They reveal two different groups of systems: one with short orbital periods (P< 1000 d) and mostly circular or almost circular orbits, and another with longer period and eccentric (e> 0.1) orbits. These two groups either

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

PubMed Central

2011-01-01

Background Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of Drosophila melanogaster. Results Both technologies produce highly reproducible profiles within each platform, ChIP-seq generally produces profiles with a better signal-to-noise ratio, and allows detection of more peaks and narrower peaks. The set of peaks identified by the two technologies can be significantly different, but the extent to which they differ varies depending on the factor and the analysis algorithm. Importantly, we found that there is a significant variation among multiple sequencing profiles of input DNA libraries and that this variation most likely arises from both differences in experimental condition and sequencing depth. We further show that using an inappropriate input DNA profile can impact the average signal profiles around genomic features and peak calling results, highlighting the importance of having high quality input DNA data for normalization in ChIP-seq analysis. Conclusions Our findings highlight the biases present in each of the platforms, show the variability that can arise from both technology and analysis methods, and emphasize the importance of obtaining high quality and deeply sequenced input DNA libraries for ChIP-seq analysis. PMID:21356108

Resolved 12CH2D2 and 13CH3D in CH4 as Sensitive Indicators of Disequilibrium and Equilibrium during Microbial Methane Cycling

NASA Astrophysics Data System (ADS)

Ash, J. L.; Egger, M.; Slomp, C. P.; Kohl, I. E.; Treude, T.; Rumble, D.; Young, E. D.

2016-12-01

The ability to measure the relative concentrations of at least two doubly-substituted rare isotopologues of gases with biogeochemical relevance provides new constraints on sources and sinks of these gases. In particular, as shown recently for O2, the use of two independent, rare isotopologues allows for detection of thermodynamic intra-species equilibrium and disequilibrium. Here, we report the first measurements of fully resolved 13CH3D and 12CH2D2 from natural samples of microbial methane gas. A suite of sedimentary methane samples from the Bornholm Basin in the Baltic Sea was collected during IODP Exp. 347. Sample depths range from 2-20 meters below seafloor (mbsf). Methane concentrations decrease with depth, and mcrA (a marker for methanogenesis and methanotropy) is present throughout. See Figure. Both Δ13CH3D and Δ12CH2D2 increase with depth as methane concentrations decrease with the shallowest samples exhibiting disequilibrium by up to 2‰ in Δ13CH3D and 13‰ in Δ12CH2D2 while the deepest samples approach isotopic thermodynamic equilibrium (marked by grey bars in Figure). The Fe-mediated anaerobic oxidation of methane (Fe-AOM) has been inferred in these sediments by geochemical modeling . Slow methane cycling by methanogensis and methanotrophy is likely responsible for the approach to isotopic bond order equilibrium in CH4 with depth, consistent with Fe-AOM. While axenic culturing experiments generate methane with large deficits in 12CH2D2 (reported at this meeting), these data from the Baltic Sea demonstrate that isotopic equilibrium can be achieved during microbial recycling of methane. In the absence of Δ12CH2D2, the Δ13CH3D values alone could be misinterpreted as representing gradients in temperature due perhaps to exothermic organic matter degradation. The combination of both mass-18 rare isotopologues of methane provides the means to distinguish equilibrium from disequilibrium and probe microbial methane cycling even where Δ13CH3D suggests

Diminished CAGE Effect in {p}-H2: Infrared Spectra of CH3S Observed from Photolysis of CH3SH, CH3SCH3, and CH3SSCH3 Isolated in {p}-H2

NASA Astrophysics Data System (ADS)

Lee, Yuan-Pern; Bahou, Mohammed

2010-06-01

We report infrared absorption spectrum of the methylthio (or thiomethoxy) radical, CH3S, isolated in solid {p}-H2. CH3S was produced by in situ UV photodissociation of three precursors: CH3SH, CH3SH3, and CH3SSCH3 isolated in solid {p}-H2. New absorption features commonly observed with similar intensity ratios in experiments using these precursors are assigned as absorption of CH3S. In Addition to the previously assigned transitions of ν 3 (a1) at 727.1 cm-1, fundamental transitions ν 6 (a1) at 771.1, ν 6 (e) at 1056.6, ν 5 (a1) at 1400.0, and &nu 4 (a1) at 2898.0 cm-1 were observed. The wavenumbers of these features agree satisfactorily with those predicted with a spin-vibronic Hamiltonian accounting for the anharmonic effects and the Jahn-Teller effects to the qu rtic term; the corresponding wavenumbers predicted from theory are ν 6 (a1) at 793, ν 6 (e) at 1105, ν 5 (a1) at 1436, and ν 4 (a1) at 2938 cm-1, with deviations of 14-4.6 % from experiments. Previous attempts of UV photolysis of CH3SCH3 and CH3SSCH3 isolated in an Ar matrix failed to produce CH3S. These results serve as an excellent example that the diminished cae effect of solid {p}-H2 makes production of free radicals via photolysis in situ feasible. If time permits, other examples will be discussed. A. V. Marenich and J. E. Boggs, J. Chem. Theory Comput., 1, 1162 (2005).

Effects of Boreal Lake Wetlands on Atmospheric 13CH3D and 12CH2D2

NASA Astrophysics Data System (ADS)

Haghnegahdar, M. A.; Kohl, I. E.; Schauble, E. A.; Walter Anthony, K. M.; Young, E. D.

2017-12-01

Recently, we developed a theoretical model to investigate the potential use of 13CH3D and 12CH2D2 as tools for tracking atmospheric methane budget. We used electronic structure methods to estimate kinetic isotope fractionations associated with the major sink reactions of CH4 in air (reactions with •OH and Cl•), and literature data with reconnaissance measurements of the relative abundances of 13CH3D and 12CH2D2 to estimate the compositions of the largest atmospheric sources. Here we present new methane rare isotopologue data from boreal wetlands, comprising one of the most important sources, in order to evaluate the robustness of the model. Boreal wetlands (>55° N) account for more than half of the wetland area in the Northern hemisphere. We analyzed methane samples from high latitude lakes representing different geographical regions, geological and ecological contexts, methane fluxes, and isotopic signatures. Using clumped isotopes of CH4 we are able to determine the likely production mechanism for natural CH4 samples. So far, all of our analyzed samples except one plot in the microbial pure-culture methanogenesis field (Young et al. 2017) with ranges of -0.2‰ to +1.2‰ for Δ13CH3D, and -29.6‰ to -18.2‰ for Δ12CH2D2. These compositions are far from equilibrium. The one exception, from Lake Doughnut, Alaska, exhibits Δ13CH3D and Δ12CH2D2 values of +5.2‰ and +18.7‰, respectively, which fall near ambient thermodynamic equilibrium values. This may be an effect of methanotrophy. Mean Δ13CH3D and Δ12CH2D2 for all lake samples are +1.7‰ and -15.4‰ respectively, compared to our original estimate of +6.1‰ and +21.2‰ for the wetland methane source based on an assumption of equilibrium. If we assume that these samples are representative of the overall wetland source, Δ13CH3D decreases by 0.8‰ and Δ12CH2D2 decreases by 0.6‰ in our model of bulk atmospheric methane. Δ13CH3D and Δ12CH2D2 values of air (including •OH and Cl• sink

ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data.

PubMed

Ravanmehr, Vida; Kim, Minji; Wang, Zhiying; Milenkovic, Olgica

2018-03-15

Chromatin immunoprecipitation sequencing (ChIP-seq) experiments are inexpensive and time-efficient, and result in massive datasets that introduce significant storage and maintenance challenges. To address the resulting Big Data problems, we propose a lossless and lossy compression framework specifically designed for ChIP-seq Wig data, termed ChIPWig. ChIPWig enables random access, summary statistics lookups and it is based on the asymptotic theory of optimal point density design for nonuniform quantizers. We tested the ChIPWig compressor on 10 ChIP-seq datasets generated by the ENCODE consortium. On average, lossless ChIPWig reduced the file sizes to merely 6% of the original, and offered 6-fold compression rate improvement compared to bigWig. The lossy feature further reduced file sizes 2-fold compared to the lossless mode, with little or no effects on peak calling and motif discovery using specialized NarrowPeaks methods. The compression and decompression speed rates are of the order of 0.2 sec/MB using general purpose computers. The source code and binaries are freely available for download at https://github.com/vidarmehr/ChIPWig-v2, implemented in C ++. milenkov@illinois.edu. Supplementary data are available at Bioinformatics online.

New assignments in the 2 μm transparency window of the 12CH4 Octad band system

NASA Astrophysics Data System (ADS)

Daumont, L.; Nikitin, A. V.; Thomas, X.; Régalia, L.; Von der Heyden, P.; Tyuterev, Vl. G.; Rey, M.; Boudon, V.; Wenger, Ch.; Loëte, M.; Brown, L. R.

2013-02-01

This paper reports new assignments of rovibrational transitions of 12CH4 bands in the range 4600-4887 cm-1 which is usually referred to as a part of the 2 μm methane transparency window. Several experimental data sources for methane line positions and intensities were combined for this analysis. Three long path Fourier transform spectra newly recorded in Reims with 1603 m absorption path length and pressures of 1, 7 and 34 hPa for samples of natural abundance CH4 provided new measurements of 12CH4 lines. Older spectra for 13CH4 (90% purity) from JPL with 73 m absorption path length were used to identify the corresponding lines. Most of the lines in this region belong to the Octad system of 12CH4. The new spectra allowed us to assign 1014 new line positions and to measure 1095 line intensities in the cold bands of the Octad. These new line positions and intensities were added to the global fit of Hamiltonian and dipole moment parameters of the Ground State, Dyad, Pentad and Octad systems. This leads to a noticeable improvement of the theoretical description in this methane transparency window and a better global prediction of the methane spectrum.

Effects of coastal marsh conversion to shrimp aquaculture ponds on CH4 and N2O emissions

NASA Astrophysics Data System (ADS)

Yang, P.; Bastviken, D.; Lai, D. Y. F.; Jin, B. S.; Mou, X. J.; Tong, C.; Yao, Y. C.

2017-12-01

In this study, we compared the CH4 and N2O fluxes from a tidal brackish Cyperus malaccensis marsh ecosystem and nearby shrimp ponds, converted from C. malaccensis marsh in the last 3-4 years, in the Min River estuary of southeast China over the aquaculture period of the year. Significant differences in CH4 and N2O fluxes were observed in space (between brackish marsh and shrimp ponds) and in time (between sampling occasions that were distributed over the aquaculture period). CH4 fluxes from the shrimp ponds were on an average 10-fold higher than from the brackish marsh. N2O emissions, on the other hand, were lower from the shrimp pond (25% of the emissions from the brackish marsh). Accessory data indicates that these patterns were primarily linked to water level variability and temperature (all fluxes), sediment porewater sulfate concentrations (CH4 flux) and total nitrogen concentrations (N2O flux). Our research demonstrates that the coastal marsh ecosystem converted to aquaculture ponds considerably alter emissions of CH4 and N2O and provides input to the global discussion on how to account for emissions from various types of flooded land in greenhouse gas inventories.

Martian CH(4): sources, flux, and detection.

PubMed

Onstott, T C; McGown, D; Kessler, J; Lollar, B Sherwood; Lehmann, K K; Clifford, S M

2006-04-01

Recent observations have detected trace amounts of CH(4) heterogeneously distributed in the martian atmosphere, which indicated a subsurface CH(4) flux of ~2 x 10(5) to 2 x 10(9) cm(2) s(1). Four different origins for this CH(4) were considered: (1) volcanogenic; (2) sublimation of hydrate- rich ice; (3) diffusive transport through hydrate-saturated cryosphere; and (4) microbial CH(4) generation above the cryosphere. A diffusive flux model of the martian crust for He, H(2), and CH(4) was developed based upon measurements of deep fracture water samples from South Africa. This model distinguishes between abiogenic and microbial CH(4) sources based upon their isotopic composition, and couples microbial CH(4) production to H(2) generation by H(2)O radiolysis. For a He flux of approximately 10(5) cm(2) s(1) this model yields an abiogenic CH(4) flux and a microbial CH(4) flux of approximately 10(6) and approximately 10(9) cm(2) s(1), respectively. This flux will only reach the martian surface if CH(4) hydrate is saturated in the cryosphere; otherwise it will be captured within the cryosphere. The sublimation of a hydrate-rich cryosphere could generate the observed CH(4) flux, whereas microbial CH(4) production in a hypersaline environment above the hydrate stability zone only seems capable of supplying approximately 10(5) cm(2) s(1) of CH(4). The model predicts that He/H(2)/CH(4)/C(2)H(6) abundances and the C and H isotopic values of CH(4) and the C isotopic composition of C(2)H(6) could reveal the different sources. Cavity ring-down spectrometers represent the instrument type that would be most capable of performing the C and H measurements of CH(4) on near future rover missions and pinpointing the cause and source of the CH(4) emissions.

Contrast between the mechanisms for dissociative electron attachment to CH3SCN and CH3NCS.

PubMed

Miller, Thomas M; Viggiano, Albert A; Shuman, Nicholas S

2018-05-14

The kinetics of thermal electron attachment to methyl thiocyanate (CH 3 SCN), methyl isothiocyanate (CH 3 NCS), and ethyl thiocyanate (C 2 H 5 SCN) were measured using flowing afterglow-Langmuir probe apparatuses at temperatures between 300 and 1000 K. CH 3 SCN and C 2 H 5 SCN undergo inefficient dissociative attachment to yield primarily SCN - at 300 K (k = 2 × 10 -10 cm 3 s -1 ), with increasing efficiency as temperature increases. The increase is well described by activation energies of 0.17 eV (CH 3 SCN) and 0.14 eV (C 2 H 5 SCN). CN - product is formed at <1% branching at 300 K, increasing to ∼30% branching at 1000 K. Attachment to CH 3 NCS yields exclusively SCN - ionic product but at a rate at 300 K that is below our detection threshold (k < 10 -12 cm 3 s -1 ). The rate coefficient increases rapidly with increasing temperature (k = 6 × 10 -11 cm 3 s -1 at 600 K), in a manner well described by an activation energy of 0.51 eV. Calculations at the B3LYP/def2-TZVPPD level suggest that attachment to CH 3 SCN proceeds through a dissociative state of CH 3 SCN - , while attachment to CH 3 NCS initially forms a weakly bound transient anion CH 3 NCS -* that isomerizes over an energetic barrier to yield SCN - . Kinetic modeling of the two systems is performed in an attempt to identify a kinetic signature differentiating the two mechanisms. The kinetic modeling reproduces the CH 3 NCS data only if dissociation through the transient anion is considered.

Contrast between the mechanisms for dissociative electron attachment to CH3SCN and CH3NCS

NASA Astrophysics Data System (ADS)

Miller, Thomas M.; Viggiano, Albert A.; Shuman, Nicholas S.

2018-05-01

The kinetics of thermal electron attachment to methyl thiocyanate (CH3SCN), methyl isothiocyanate (CH3NCS), and ethyl thiocyanate (C2H5SCN) were measured using flowing afterglow-Langmuir probe apparatuses at temperatures between 300 and 1000 K. CH3SCN and C2H5SCN undergo inefficient dissociative attachment to yield primarily SCN- at 300 K (k = 2 × 10-10 cm3 s-1), with increasing efficiency as temperature increases. The increase is well described by activation energies of 0.17 eV (CH3SCN) and 0.14 eV (C2H5SCN). CN- product is formed at <1% branching at 300 K, increasing to ˜30% branching at 1000 K. Attachment to CH3NCS yields exclusively SCN- ionic product but at a rate at 300 K that is below our detection threshold (k < 10-12 cm3 s-1). The rate coefficient increases rapidly with increasing temperature (k = 6 × 10-11 cm3 s-1 at 600 K), in a manner well described by an activation energy of 0.51 eV. Calculations at the B3LYP/def2-TZVPPD level suggest that attachment to CH3SCN proceeds through a dissociative state of CH3SCN-, while attachment to CH3NCS initially forms a weakly bound transient anion CH3NCS-* that isomerizes over an energetic barrier to yield SCN-. Kinetic modeling of the two systems is performed in an attempt to identify a kinetic signature differentiating the two mechanisms. The kinetic modeling reproduces the CH3NCS data only if dissociation through the transient anion is considered.

Petroleum degradation by Pseudomonas sp. ZS1 is impeded in the presence of antagonist Alcaligenes sp. CT10.

PubMed

Liang, Jibei; Cheng, Tao; Huang, Yi; Liu, Jianhua

2018-05-28

Enhanced bioremediation is a favorable approach for petroleum pollutant cleanup, which depends on the growth of oil-eating microorganisms. In this study, we show that, by using the modified T-RFLP (mT-RFLP) methodology, one of the four major microbial populations derived from oil sludge has failed to propagate in MS medium supplemented with 2% yeast extract (YE). rDNA sequence-based analysis indicated that the four populations were Donghicola sp. CT5, Bacillus sp. CT6, Alcaligenes sp. CT10, and Pseudomonas sp. ZS1. Four purified strains grow well individually in MS medium supplemented with 2% YE, suggesting that ZS1 growth is antagonized by other strains. Co-growth analysis using mT-RFLP methodology and plate inhibitory assay indicated that ZS1 exhibited antagonistic effect against CT5 and CT6. On the other hand, co-growth analysis and plate inhibition assay showed that CT10 antagonized against ZS1. To investigate the potential compounds responsible for the antagonism, supernatant of CT10 culture was subjected to GC-MS analysis. Analysis indicated that CT10 produced a number of antimicrobial compounds including cyclodipeptide c-(L-Pro-L-Phe), which was known to inhibit the growth of Pseudomonas sp. Growth test using the purified c-(L-Pro-L-Phe) from CT10 confirmed its inhibitory activity. We further showed that, using both gravimetric and GC analysis, CT10 antagonism against the oil-eating ZS1 led to the diminishing of crude oil degradation. Together, our results indicate that bioremediation can be affected by environmental antagonists.

Sequential ChIP Protocol for Profiling Bivalent Epigenetic Modifications (ReChIP).

PubMed

Desvoyes, Bénédicte; Sequeira-Mendes, Joana; Vergara, Zaida; Madeira, Sofia; Gutierrez, Crisanto

2018-01-01

Identification of chromatin modifications, e.g., histone acetylation and methylation, among others, is widely carried out by using a chromatin immunoprecipitation (ChIP) strategy. The information obtained with these procedures is useful to gain an overall picture of modifications present in all cells of the population under study. It also serves as a basis to figure out the mechanisms of chromatin organization and gene regulation at the population level. However, the ultimate goal is to understand gene regulation at the level of single chromatin fibers. This requires the identification of chromatin modifications that occur at a given genomic location and within the same chromatin fiber. This is achieved by following a sequential ChIP strategy using two antibodies to distinguish different chromatin modifications. Here, we describe a sequential ChIP protocol (Re-ChIP), paying special attention to the controls needed and the required steps to obtain meaningful and reproducible results. The protocol is developed for young Arabidopsis seedlings but could be adapted to other plant materials.

Flux and distribution of methane (CH4) in the Gunsan Basin of the southeastern Yellow Sea, off the Western Korea.

PubMed

Lee, Jun-Ho; Woo, Han Jun; Son, Seung-Kyu; Kim, Moonkoo; Lee, Dong-Hun; Tsunogai, Urumu; Jeong, Kap-Sik

2018-04-16

The flux and distribution of methane (CH 4 ) was investigated in the seawater column at 14 stations in the Gunsan Basin, the southeastern part of Yellow Sea from 2013 to 2015. Here CH 4 is concentrated 2.4-4.7 (3.4 ± 0.7) nM in the surface and 2.5-7.4 (5.2 ± 1.7) nM in the bottom layer. The CH 4 saturation ratios ranged from 65.5% to 295.5% (162.6 ± 68.7), comprising the mean sea-to-air CH 4 flux of 3.8 to 25.3 (15.6 ± 5.5) µM m -2 d -1 . Methane concentration was largely different in the upper and the lower seawater layers that is separated by the thermocline of which depth is variable (20-60 m) depending on the time of sampling. The concentration of seawater dissolved CH 4 is high between the bottom surface of the thermocline layer and the sea floor. Generally it tends to decrease from the south-westernmost part of the basin toward the west coast of Korea. This distribution pattern of CH 4 seems to result from the CH 4 supply by decomposition of organic matters produced in the upper seawater layer that is superimposed by the larger supply from the underlying sediment layer especially beneath the thermocline. The latter is manifested by ubiquitous CH 4 seeps from the seafloor sediments.

In-plane chemical pressure essential for superconductivity in BiCh2-based (Ch: S, Se) layered structure

PubMed Central

Mizuguchi, Yoshikazu; Miura, Akira; Kajitani, Joe; Hiroi, Takafumi; Miura, Osuke; Tadanaga, Kiyoharu; Kumada, Nobuhiro; Magome, Eisuke; Moriyoshi, Chikako; Kuroiwa, Yoshihiro

2015-01-01

BiCh2-based compounds (Ch: S, Se) are a new series of layered superconductors, and the mechanisms for the emergence of superconductivity in these materials have not yet been elucidated. In this study, we investigate the relationship between crystal structure and superconducting properties of the BiCh2-based superconductor family, specifically, optimally doped Ce1−xNdxO0.5F0.5BiS2 and LaO0.5F0.5Bi(S1−ySey)2. We use powder synchrotron X-ray diffraction to determine the crystal structures. We show that the structure parameter essential for the emergence of bulk superconductivity in both systems is the in-plane chemical pressure, rather than Bi-Ch bond lengths or in-plane Ch-Bi-Ch bond angle. Furthermore, we show that the superconducting transition temperature for all REO0.5F0.5BiCh2 superconductors can be determined from the in-plane chemical pressure. PMID:26447333

Direct observation of unimolecular decay of CH{sub 3}CH{sub 2}CHOO Criegee intermediates to OH radical products

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

Fang, Yi; Liu, Fang; Lester, Marsha I., E-mail: milester@sas.upenn.edu

2016-07-28

The unimolecular decay of carbonyl oxide intermediates, known as Criegee intermediates, produced in alkene ozonolysis is a significant source of OH radicals in the troposphere. Here, the rate of appearance of OH radical products is examined directly in the time-domain for a prototypical alkyl-substituted Criegee intermediate, CH{sub 3}CH{sub 2}CHOO, following vibrational activation under collision-free conditions. Complementary statistical Rice–Ramsperger–Kassel–Marcus calculations of the microcanonical unimolecular decay rate for CH{sub 3}CH{sub 2}CHOO are also carried out at energies in the vicinity of the barrier for 1,4 hydrogen atom transfer that leads to OH products. Tunneling through the barrier, derived from high level electronicmore » structure calculations, contributes significantly to the decay rate. Infrared transitions of CH{sub 3}CH{sub 2}CHOO are identified in the CH stretch overtone region, which are detected by ultraviolet laser-induced fluorescence of the resultant OH products. The features observed are attributed to CH vibrational excitations and conformational forms utilizing insights from theory. Both experiment and theory yield unimolecular decay rates for CH{sub 3}CH{sub 2}CHOO of ca. 10{sup 7} s{sup −1}, which are slower than those obtained for syn-CH{sub 3}CHOO or (CH{sub 3}){sub 2}COO reported previously [Fang et al., J. Chem. Phys. 144, 061102 (2016)] at similar energies. Master equation modeling is also utilized to predict the thermal decay rate of CH{sub 3}CH{sub 2}CHOO under atmospheric conditions, giving a rate of 279 s{sup −1} at 298 K.« less

Enzyme-catalyzed synthesis of poly[(R)-(-)-3-hydroxybutyrate]: Formation of macroscopic granules in vitro

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

Gerngross, T.U.; Martin, D.P.

A combined chemical and enzymatic procedure has been developed to synthesize macroscopic poly[(R)-(-)-3-hydroxybutyrate] (PHB) granules in vitro. The granules form in a matter of minutes when purified polyhydroxyalkanoate (PHA) synthase from Alcaligenes eutrophus is exposed to synthetically prepared (R)-3-hydroxybutyryl coenzyme A, thereby establishing the minimal requirements for PHB granule formation. The artificial granules are spherical with diameters of up to 3 {mu}m and significantly larger than their native counterparts (0.5 {mu}m). The isolated PHB was characterized by {sup 1}H and {sup 13}C NMR, gel-permeation chromatography, and chemical analysis. The in vitro polymerization system yields PHB with a molecular mass >more » 10 x 10{sup 6} Da, exceeding by an order of magnitude the mass of PHAs typically extracted from microorganisms. We also demonstrate that the molecular mass of the polymer can be controlled by the initial PHA synthase concentration. Preliminary kinetic analysis of de novo granule formation confirms earlier findings of a lag time for the enzyme but suggests the involvement of an additional granule assembly step. Minimal requirements for substrate recognition were investigated. Since substrate analogs lacking the adenosine 3{prime}, 5{prime}-bisphosphate moiety of (R)-3-hydroxybutyryl coenzyme A were not accepted by the PHA synthase, we provide evidence that this structural element of the substrate is essential for catalysis. PHAs provide a range of natural, renewable, biodegradable thermoplastics with a broad range of useful material properties. 33 refs., 6 figs., 1 tab.« less

Characterization of a chromosomally encoded 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase from Burkholderia sp. strain RASC.

PubMed Central

Suwa, Y; Wright, A D; Fukimori, F; Nummy, K A; Hausinger, R P; Holben, W E; Forney, L J

1996-01-01

The findings of previous studies indicate that the genes required for metabolism of the pesticide 2,4-dichlorophenoxyacetic acid (2,4-D) are typically encoded on broad-host-range plasmids. However, characterization of plasmid-cured strains of Burkholderia sp. strain RASC, as well as mutants obtained by transposon mutagenesis, suggested that the 2,4-D catabolic genes were located on the chromosome of this strain. Mutants of Burkholderia strain RASC unable to degrade 2,4-D (2,4-D- strains) were obtained by insertional inactivation with Tn5. One such mutant (d1) was shown to have Tn5 inserted in tfdARASC, which encodes 2,4-D/alpha-ketoglutarate dioxygenase. This is the first reported example of a chromosomally encoded tfdA. The tfdARASC gene was cloned from a library of wild-type Burkholderia strain RASC DNA and shown to express 2,4-D/alpha-ketoglutarate dioxygenase activity in Escherichia coli. The DNA sequence of the gene was determined and shown to be similar, although not identical, to those of isofunctional genes from other bacteria. Moreover, the gene product (TfdARASC) was purified and shown to be similar in molecular weight, amino-terminal sequence, and reaction mechanism to the canonical TfdA of Alcaligenes eutrophus JMP134. The data presented here indicate that tfdA genes can be found on the chromosome of some bacterial species and suggest that these catabolic genes are rather mobile and may be transferred by means other than conjugation. PMID:8779585

Proton-coupled electron transfer in the catalytic cycle of Alcaligenes xylosoxidans copper-dependent nitrite reductase.

PubMed

Leferink, Nicole G H; Han, Cong; Antonyuk, Svetlana V; Heyes, Derren J; Rigby, Stephen E J; Hough, Michael A; Eady, Robert R; Scrutton, Nigel S; Hasnain, S Samar

2011-05-17

We demonstrated recently that two protons are involved in reduction of nitrite to nitric oxide through a proton-coupled electron transfer (ET) reaction catalyzed by the blue Cu-dependent nitrite reductase (Cu NiR) of Alcaligenes xylosoxidans (AxNiR). Here, the functionality of two putative proton channels, one involving Asn90 and the other His254, is studied using single (N90S, H254F) and double (N90S--H254F) mutants. All mutants studied are active, indicating that protons are still able to reach the active site. The H254F mutation has no effect on the catalytic activity, while the N90S mutation results in ~70% decrease in activity. Laser flash-photolysis experiments show that in H254F and wild-type enzyme electrons enter at the level of the T1Cu and then redistribute between the two Cu sites. Complete ET from T1Cu to T2Cu occurs only when nitrite binds at the T2Cu site. This indicates that substrate binding to T2Cu promotes ET from T1Cu, suggesting that the enzyme operates an ordered mechanism. In fact, in the N90S and N90S--H254F variants, where the T1Cu site redox potential is elevated by ∼60 mV, inter-Cu ET is only observed in the presence of nitrite. From these results it is evident that the Asn90 channel is the main proton channel in AxNiR, though protons can still reach the active site if this channel is disrupted. Crystallographic structures provide a clear structural rationale for these observations, including restoration of the proton delivery via a significant movement of the loop connecting the T1Cu ligands Cys130 and His139 that occurs on binding of nitrite. Notably, a role for this loop in facilitating interaction of cytochrome c(551) with Cu NiR has been suggested previously based on a crystal structure of the binary complex.

Thermochemistry and kinetics for 2-butanone-1-yl radical (CH2·C(═O)CH2CH3) reactions with O2.

PubMed

Sebbar, N; Bozzelli, J W; Bockhorn, H

2014-01-09

Thermochemistry of reactants, intermediates, transition state structures, and products along with kinetics on the association of CH2·C(═O)CH2CH3 (2-butanone-1-yl) with O2 and dissociation of the peroxy adduct isomers are studied. Thermochemical properties are determined using ab initio (G3MP2B3 and G3) composite methods along with density functional theory (B3LYP/6-311g(d,p)). Entropy and heat capacity contributions versus temperature are determined from structures, vibration frequencies, and internal rotor potentials. The CH2·C(═O)CH2CH3 radical + O2 association results in a chemically activated peroxy radical with 27 kcal mol(-1) excess of energy. The chemically activated adduct can react to stabilized peroxy or hydroperoxide alkyl radical adducts, further react to lactones plus hydroxyl radical, or form olefinic ketones and a hydroperoxy radical. Kinetic parameters are determined from the G3 composite methods derived thermochemical parameters, and quantum Rice-Ramsperger-Kassel (QRRK) analysis to calculate k(E) with master equation analysis to evaluate falloff in the chemically activated and dissociation reactions. One new, not previously reported, peroxy chemistry reaction is presented. It has a low barrier path and involves a concerted reaction resulting in olefin formation, H2O elimination, and an alkoxy radical.

Computing energy levels of CH4, CHD3, CH3D, and CH3F with a direct product basis and coordinates based on the methyl subsystem.

PubMed

Zhao, Zhiqiang; Chen, Jun; Zhang, Zhaojun; Zhang, Dong H; Wang, Xiao-Gang; Carrington, Tucker; Gatti, Fabien

2018-02-21

Quantum mechanical calculations of ro-vibrational energies of CH 4 , CHD 3 , CH 3 D, and CH 3 F were made with two different numerical approaches. Both use polyspherical coordinates. The computed energy levels agree, confirming the accuracy of the methods. In the first approach, for all the molecules, the coordinates are defined using three Radau vectors for the CH 3 subsystem and a Jacobi vector between the remaining atom and the centre of mass of CH 3 . Euler angles specifying the orientation of a frame attached to CH 3 with respect to a frame attached to the Jacobi vector are used as vibrational coordinates. A direct product potential-optimized discrete variable vibrational basis is used to build a Hamiltonian matrix. Ro-vibrational energies are computed using a re-started Arnoldi eigensolver. In the second approach, the coordinates are the spherical coordinates associated with four Radau vectors or three Radau vectors and a Jacobi vector, and the frame is an Eckart frame. Vibrational basis functions are products of contracted stretch and bend functions, and eigenvalues are computed with the Lanczos algorithm. For CH 4 , CHD 3 , and CH 3 D, we report the first J > 0 energy levels computed on the Wang-Carrington potential energy surface [X.-G. Wang and T. Carrington, J. Chem. Phys. 141(15), 154106 (2014)]. For CH 3 F, the potential energy surface of Zhao et al. [J. Chem. Phys. 144, 204302 (2016)] was used. All the results are in good agreement with experimental data.

Computing energy levels of CH4, CHD3, CH3D, and CH3F with a direct product basis and coordinates based on the methyl subsystem

NASA Astrophysics Data System (ADS)

Zhao, Zhiqiang; Chen, Jun; Zhang, Zhaojun; Zhang, Dong H.; Wang, Xiao-Gang; Carrington, Tucker; Gatti, Fabien

2018-02-01

Quantum mechanical calculations of ro-vibrational energies of CH4, CHD3, CH3D, and CH3F were made with two different numerical approaches. Both use polyspherical coordinates. The computed energy levels agree, confirming the accuracy of the methods. In the first approach, for all the molecules, the coordinates are defined using three Radau vectors for the CH3 subsystem and a Jacobi vector between the remaining atom and the centre of mass of CH3. Euler angles specifying the orientation of a frame attached to CH3 with respect to a frame attached to the Jacobi vector are used as vibrational coordinates. A direct product potential-optimized discrete variable vibrational basis is used to build a Hamiltonian matrix. Ro-vibrational energies are computed using a re-started Arnoldi eigensolver. In the second approach, the coordinates are the spherical coordinates associated with four Radau vectors or three Radau vectors and a Jacobi vector, and the frame is an Eckart frame. Vibrational basis functions are products of contracted stretch and bend functions, and eigenvalues are computed with the Lanczos algorithm. For CH4, CHD3, and CH3D, we report the first J > 0 energy levels computed on the Wang-Carrington potential energy surface [X.-G. Wang and T. Carrington, J. Chem. Phys. 141(15), 154106 (2014)]. For CH3F, the potential energy surface of Zhao et al. [J. Chem. Phys. 144, 204302 (2016)] was used. All the results are in good agreement with experimental data.

HIGH-ENERGY ELECTRON IRRADIATION OF INTERSTELLAR CARBONACEOUS DUST ANALOGS: COSMIC-RAY EFFECTS ON THE CARRIERS OF THE 3.4 μ m ABSORPTION BAND

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

Maté, Belén; Molpeceres, Germán; Jiménez-Redondo, Miguel

2016-11-01

The effects of cosmic rays on the carriers of the interstellar 3.4 μ m absorption band have been investigated in the laboratory. This band is attributed to stretching vibrations of CH{sub 3} and CH{sub 2} in carbonaceous dust. It is widely observed in the diffuse interstellar medium, but disappears in dense clouds. Destruction of CH{sub 3} and CH{sub 2} by cosmic rays could become relevant in dense clouds, shielded from the external ultraviolet field. For the simulations, samples of hydrogenated amorphous carbon (a-C:H) have been irradiated with 5 keV electrons. The decay of the band intensity versus electron fluence reflectsmore » a-C:H dehydrogenation, which is well described by a model assuming that H{sub 2} molecules, formed by the recombination of H atoms liberated through CH bond breaking, diffuse out of the sample. The CH bond destruction rates derived from the present experiments are in good accordance with those from previous ion irradiation experiments of HAC. The experimental simplicity of electron bombardment has allowed the use of higher-energy doses than in the ion experiments. The effects of cosmic rays on the aliphatic components of cosmic dust are found to be small. The estimated cosmic-ray destruction times for the 3.4 μ m band carriers lie in the 10{sup 8} yr range and cannot account for the disappearance of this band in dense clouds, which have characteristic lifetimes of 3 × 10{sup 7} yr. The results invite a more detailed investigation of the mechanisms of CH bond formation and breaking in the intermediate region between diffuse and dense clouds.« less

CH_{4} production in the deep soil as a source of stem CH_{4} emission in Fagus sylvatica}

NASA Astrophysics Data System (ADS)

Maier, Martin; Machacova, Katerina; Urban, Otmar; Lang, Friederike

2017-04-01

Predicting greenhouse gas (GHG) fluxes on a global scale requires understanding fluxes on the local scale. Understanding GHG processes in soil-plant-atmosphere systems is essential to understand and mitigate GHG fluxes on the local scale. Forests are known to act as carbon sink. Yet, trees at waterlogged sites are known to emit large amounts of CH4, what can offset the positive GHG balance due the CO2 that is sequestered as wood. Generally, upland trees like European beech (Fagus sylvatica L.) are assumed not to emit CH4, and the upland forest soils are regarded as CH4 sinks. Soil-atmosphere fluxes and stem-atmosphere fluxes of CH4 were studied together with soil gas profiles at two upland beech forest sites in Germany and Czech Republic. Soil was a net CH4 sink at both sites. While most trees showed no or low emissions, one beech tree had exorbitant CH4 emissions that were higher than the CH4 sink capacity of the soil. A soil survey showed strong redoximorphic color patterns in the soil adjacent to this tree. Although the soil around the tree was taking up CH4, the soil gas profiles around this tree showed CH4 production at a soil depth >0.3 m. We interpret the coincidence of the production of CH4 in the deep soil below the beech with the large stem emissions as strong hint that there is a transport link between the soil and stem. We think that the root system represents a preferential transport system for CH4 despite the fact that beech roots usually do not have a special gas transport tissue. The observed CH4 stem emissions represent an important CH4 flux in this ecosystem, and, thus, should be considered in future research. Acknowledgement This research was supported by the Czech Academy of Sciences and the German Academic Exchange Service within the project "Methane (CH4) and nitrous oxide (N2O) emissions from Fagus sylvatica trees" (DAAD-15-03), the Czech Science Foundation (17-18112Y), National Programme for Sustainability I (LO1415) and project DFG (MA 5826

Experimental and Computational Study fo CH, CH*, and OH* in an Axisymmetric Laminar Diffusion Flame

NASA Technical Reports Server (NTRS)

Walsh, K. T.

1998-01-01

In this study, we extend the results of previous combined numerical and experimental investigations of an axisymmetric laminar diffusion flame in which difference Raman spectroscopy, laser-induced fluorescence (LIF), and a multidimensional flame model were used to generate profiles of the temperature and major and minor species. A procedure is outlined by which the number densities of ground-state CH (X(sup 2)II) excited-state CH (A(sup 2)Delta, denoted CH*), and excited-state OH (A(sup 2)Sigma, denoted OH*) are measured and modeled. CH* and OH* number densities are deconvoluted from line-of-sight flame-emission measurements. Ground-state CH is measured using linear LIF. The computations are done with GRI Mech 2.11 as well as an alternate hydrocarbon mechanism. In both cases, additional reactions for the production and consumption of CH* and OH* are added from recent kinetic studies. Collisional quenching and spontaneous emission are responsible for the de-excitation of the excited-state radicals. As with our previous investigations, GRI Mech 2.11 continues to produce very good agreement with the overall flame length observed in the experiments, while significantly under predicting the flame lift-off height. The alternate kinetic scheme is much more accurate in predicting lift-off height but overpredicts the over-all flame length. Ground-state CH profiles predicted with GRI Mech 2.11 are in excellent agreement with the corresponding measurements, regarding both spatial distribution and absolute concentration (measured at 4 ppm) of the CH radical. Calculations of the excited-state species show reasonable agreement with the measurements as far as spatial distribution and overall characteristics are concerned. For OH*, the measured peak mole fraction, 1.3 x 10(exp -8), compared well with computed peaks, while the measured peak level for CH*, 2 x 10(exp -9), was severely underpredicted by both kinetic schemes, indicating that the formation and destruction kinetics

Infrared-Terahertz Double-Resonance Spectroscopy of CH3F and CH3Cl at Atmospheric Pressure

DTIC Science & Technology

2012-05-16

coincidence with the RQ3(6) rovibrational transition in CH3 35Cl [Fig. 4(b)]. At atmospheric pressure, nine more P -, Q-, and R-branch rovibrational...the double-resonance signatures of all IR-THz pump-probe coincidences at atmospheric pressure for 12CH3F and CH3 35Cl 052507-11050-2947/2012/85(5...were calculated using the rotational constants listed in Tables I and II. For CH3F, the standard P - type (J = − 1), Q-type (J = 0), and R-type (J

ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition.

PubMed

Zhu, Lin; Guo, Wei-Li; Deng, Su-Ping; Huang, De-Shuang

2016-01-01

In recent years, thanks to the efforts of individual scientists and research consortiums, a huge amount of chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experimental data have been accumulated. Instead of investigating them independently, several recent studies have convincingly demonstrated that a wealth of scientific insights can be gained by integrative analysis of these ChIP-seq data. However, when used for the purpose of integrative analysis, a serious drawback of current ChIP-seq technique is that it is still expensive and time-consuming to generate ChIP-seq datasets of high standard. Most researchers are therefore unable to obtain complete ChIP-seq data for several TFs in a wide variety of cell lines, which considerably limits the understanding of transcriptional regulation pattern. In this paper, we propose a novel method called ChIP-PIT to overcome the aforementioned limitation. In ChIP-PIT, ChIP-seq data corresponding to a diverse collection of cell types, TFs and genes are fused together using the three-mode pair-wise interaction tensor (PIT) model, and the prediction of unperformed ChIP-seq experimental results is formulated as a tensor completion problem. Computationally, we propose efficient first-order method based on extensions of coordinate descent method to learn the optimal solution of ChIP-PIT, which makes it particularly suitable for the analysis of massive scale ChIP-seq data. Experimental evaluation the ENCODE data illustrate the usefulness of the proposed model.

The photolysis of CH3ONO

NASA Technical Reports Server (NTRS)

Wiebe, H. A.; Heicklen, J.

1972-01-01

The photolysis of CH3ONO, alone and in the presence of NO, NO-N2 mixtures, and NO-CO mixtures was studied between 25 and 150 C. The major products are CH2O, N2O, and H2O. The quantum yields of N2O were measured. The N2O yield is large at low pressures but approaches a high-pressure limiting value of 0.055 at all temperatures as the excited CH3O produced in the primary step is stabilized by collision. In the presence of excess CO, and N2O yield drops, and CO2 is produced (though not in sufficient amounts to account for the drop in N2O). When pure CH2ONO is photolyzed, CO is produced and NO accumulates in the system. Both products are formed in related processes and result from CH3O attack on CH2O.

Spatial distribution of CH3 and CH2 radicals in a methane rf discharge

NASA Astrophysics Data System (ADS)

Sugai, H.; Kojima, H.; Ishida, A.; Toyoda, H.

1990-06-01

Spatial distributions of neutral radicals CH3 and CH2 in a capacitively coupled rf glow discharge of methane were measured by threshold ionization mass spectrometry. A strong asymmetry of the density profile was found for the CH2 radical in the high-pressure (˜100 mTorr) discharge. In addition, comprehensive measurements of electron energy distribution, ionic composition, and radical sticking coefficient were made to use as inputs to theoretical modeling of radicals in the methane plasma. The model predictions agree substantially with the measured radical distributions.

Transposon mutagenesis and cloning analysis of the pathways for degradation of 2,4-dichlorophenoxyacetic acid and 3-chlorobenzoate in Alcaligenes eutrophus JMP134(pJP4).

PubMed Central

Don, R H; Weightman, A J; Knackmuss, H J; Timmis, K N

1985-01-01

Plasmid pJP4 permits its host bacterium, strain JMP134, to degrade and utilize as sole sources of carbon and energy 3-chlorobenzoate and 2,4-dichlorophenoxyacetic acid (R. H. Don and J. M. Pemberton, J. Bacteriol. 145:681-686, 1981). Mutagenesis of pJP4 by transposons Tn5 and Tn1771 enabled localization of five genes for enzymes involved in these catabolic pathways. Four of the genes, tfdB, tfdC, tfdD, and tfdE, encoded 2,4-dichlorophenol hydroxylase, dichlorocatechol 1,2-dioxygenase, chloromuconate cycloisomerase, and chlorodienelactone hydrolase, respectively. No function has been assigned to the fifth gene, tfdF, although it may encode a trans-chlorodiene-lactone isomerase. Inactivation of genes tfdC, tfdD, and tfdE, which encode the transformation of dichlorocatechol to chloromaleylacetic acid, prevented host strain JMP134 from degrading both 3-chlorobenzoate and 2,4-dichlorophenoxyacetic acid, which indicates that the pathways for these two substrates utilize common enzymes for the dissimilation of chlorocatechols. Studies with cloned catabolic genes from pJP4 indicated that whereas all essential steps in the degradation of 2,4-dichlorophenoxyacetic acid are plasmid encoded, the conversion of 3-chlorobenzoate to chlorocatechol is specified by chromosomal genes. PMID:2981813

Thz Spectroscopy of 12CH^+, 13CH^+, and 12CD^+

NASA Astrophysics Data System (ADS)

Yu, Shanshan; Drouin, Brian; Pearson, John; Amano, Takayoshi

2015-06-01

In 1937, Dunham detected a couple of unidentified lines in near-UV, and later Douglas and Herzberg identified them based on their laboratory observations to be low-J electronic transitions of CH^+. The electronic spectra, in particular the A^1Π-X^1σ^+ band, have been investigated extensively. On the other hand, the pure rotational transitions have not been studied so extensively. Only the lowest rotational transition, J=1-0, was observed in the laboratory for the normal species, 13CH^+, and CD^+. Based on the laboratory frequency, CH^+ was detected in star forming regions with the Hershel space observatory. Cernicharo et al identified pure rotational transitions from J=2-1 to J=6-5 in the far-infrared region in the ISO spectrum of the planetary nebula NGC 7027. The ISO spectra, however, were of low-resolution, so high-resolution spectroscopic observation is highly desirable. In this presentation, we have extended the measurements to higher-J lines up to 2 THz. For production of CH^+, an extended negative glow discharge in a gas mixture of CH_4 (˜ 0.5 mTorr) diluted in He (˜ 60 mTorr) was used. The optimum discharge current was about 15 mA and the axial magnetic filed to 160 Gauss was applied up. The discharge cell was cooled down to liquid nitrogen temperature. Several frequency multiplier chains, developed at JPL and purchased from Virginia Diodes, were used as THz radiation sources. New THz measurements are not only useful for providing better characterization of spectroscopic properties but also will serve as starting point for astronomical observations. T. Dunham, Publ. Astron. Soc. Pac., 49,~26 (1937) A. E. Douglas and G. Herzberg, Ap. J. 94,~381 (1941) T. Amano, Ap.J.Lett., 716, L1 (2010) T. Amano, J. Chem. Phys., 133, 244305 (2010) J. Cernicharo et al., Ap. J. Lett., 483, L65 (1997)

BariumCopperChFluorine (Ch = Sulfur, Selenium, Tellurium) p-type transparent conductors

NASA Astrophysics Data System (ADS)

Zakutayev, Andriy

BaCuChF (Ch = S, Se, Te) materials are chalcogen-based transparent conductors with wide optical band gaps (2.9 -- 3.5 eV) and a high concentration of free holes (1018 -- 1020 cm-3 ) caused by the presence of copper vacancies. Chalcogen vacancies compensate copper vacancies in these materials, setting the Fermi level close to the valence band maximum. BaCuChF thin film solid solutions prepared by pulsed laser deposition (PLD) have tunable properties, such as lattice constants, conductivity and optical band gaps. BaCuSF and BaCuSeF materials also feature room-temperature stable 3D excitons with spin-orbit-split levels. BaCuTeF has forbidden lowest-energy optical transitions which extends its transparency range. BaCuChF surfaces oxidize when exposed to air, but can be protected using Ch capping layers. Polycrystalline BaCuSeF thin films have a 4.85 eV work function, a 0.11 eV hole injection barrier into ZnPc, and 0.00 eV valence band offset with ZnTe. BaCuSeF should have s similar band offset and similar interfacial properties with CdTe and Cu(InGa)Se2, and BaCuSF should have no valence band offset with Cu2ZnSnS4, according to the transitivity rule. Therefore, BaCuSeF is suitable for applications as a p-layer in organic light-emitting diodes, p-i-n double-heterojunction and tandem chalcogenide solar cells.

Carbon-Hydrogen (C-H) Bond Activation at PdIV: A Frontier in C-H Functionalization Catalysis.

PubMed

Topczewski, Joseph J; Sanford, Melanie S

2015-01-01

The direct functionalization of carbon-hydrogen (C-H) bonds has emerged as a versatile strategy for the synthesis and derivatization of organic molecules. Among the methods for C-H bond activation, catalytic processes that utilize a Pd II /Pd IV redox cycle are increasingly common. The C-H activation step in most of these catalytic cycles is thought to occur at a Pd II centre. However, a number of recent reports have suggested the feasibility of C-H cleavage occurring at Pd IV complexes. Importantly, these latter processes often result in complementary reactivity and selectivity relative to analogous transformations at Pd II . This Mini Review highlights proposed examples of C-H activation at Pd IV centres. Applications of this transformation in catalysis as well as mechanistic details obtained from stoichiometric model studies are discussed. Furthermore, challenges and future perspectives for the field are reviewed.

Methane Provenance Determined by CH2D2 and 13CH3D Abundances

NASA Astrophysics Data System (ADS)

Kohl, I. E.; Giunta, T.; Warr, O.; Ash, J. L.; Ruffine, L.; Sherwood Lollar, B.; Young, E. D.

2017-12-01

Determining the provenance of naturally occurring methane gases is of major interest to energy companies and atmospheric climate modelers, among others. Bulk isotopic compositions and other geochemical tracers sometimes fail to provide definitive determinations of sources of methane due to complications from mixing and complicated chemical pathways of origin. Recent measurements of doubly-substituted isotopologues of methane, CH2D2 (UCLA) and 13CH3D (UCLA, CalTech, and MIT) have allowed for major improvements in sourcing natural methane gases. Early work has focused on formation temperatures obtained when the relative abundances of both doubly-substituted mass-18 species are consistent with internal equilibrium. When methane gases do not plot on the thermodynamic equilibrium curve in D12CH2D2 vs D13CH3D space, temperatures determined from D13CH3D values alone are usually spurious, even when appearing reasonable. We find that the equilibrium case is actually rare and almost exclusive to thermogenic gases produced at temperatures exceeding 100°C. All other relevant methane production processes appear to generate gases that are not in isotopologue-temperature equilibrium. When gases show departures from equilibrium as determined by the relationship between CH2D2 and 13CH3D abundances, data fall within empirically defined fields representing formation pathways. These fields are thus far consistent between different geological settings and and between lab experiments and natural samples. We have now defined fields for thermogenic gas production, microbial methanogenesis, low temperature abiotic (Sabatier) synthesis and higher temperature FTT synthesis. The majority of our natural methane data can be explained by mixing between end members originating within these production fields. Mixing can appear complex, resulting in both hyper-clumped and anti-clumped isotopologue abundances. In systems where mixtures dominate and end-members are difficult to sample, mixing models

The catalytic effects of H2CO3, CH3COOH, HCOOH and H2O on the addition reaction of CH2OO + H2O → CH2(OH)OOH

NASA Astrophysics Data System (ADS)

Zhang, Tianlei; Lan, Xinguang; Wang, Rui; Roy, Soumendra; Qiao, Zhangyu; Lu, Yousong; Wang, Zhuqing

2018-07-01

The addition reaction of CH2OO + H2O → CH2(OH)OOH without and with X (X = H2CO3, CH3COOH and HCOOH) and H2O was studied at CCSD(T)/6-311+ G(3df,2dp)//B3LYP/6-311+G(2d,2p) level of theory. Our results show that X can catalyse CH2OO + H2O → CH2(OH)OOH reaction both by increasing the number of rings, and by adding the size of the ring in which ring enlargement by COOH moiety of X inserting into CH2OO...H2O is favourable one. Water-assisted CH2OO + H2O → CH2(OH)OOH can occur by H2O moiety of (H2O)2 or the whole (H2O)2 forming cyclic structure with CH2OO, where the latter form is more favourable. Because the concentration of H2CO3 is unknown, the influence of CH3COOH, HCOOH and H2O were calculated within 0-30 km altitude of the Earth's atmosphere. The results calculated within 0-5 km altitude show that H2O and HCOOH have obvious effect on enhancing the rate with the enhancement factors are, respectively, 62.47%-77.26% and 0.04%-1.76%. Within 5-30 km altitude, HCOOH has obvious effect on enhancing the title rate with the enhancement factor of 2.69%-98.28%. However, compared with the reaction of CH2OO + HCOOH, the rate of CH2OO...H2O + HCOOH is much slower.

Training Management in the CH-46E Community After MAWTS-1 Stands Down Its CH-46E Division

DTIC Science & Technology

2012-04-23

SHOULD INCLUDE THE FOREGOING STATEMENT. QUOTATION FROM, ABSTRACTION FROM, OR REPRODUCTION OF ALL OR ANY PART OF THIS DOCUMENT IS PERMITTED...HMH) currently fly either the CH-53D Sea Stallion or the CH-53E Super Stallion helicopters. Those units that fly the CH-53D Sea Stallion are in the...process of converting to the CH-53E Super Stallion or will transition the squadrons to medium lift assault support platforms.5 The HMHs currently

Degraded Land Restoration in Reinstating CH4 Sink

PubMed Central

Singh, Jay Shankar; Gupta, Vijai K.

2016-01-01

Methane (CH4), a potent greenhouse gas, contributes about one third to the global green house gas emissions. CH4-assimilating microbes (mostly methanotrophs) in upland soils play very crucial role in mitigating the CH4 release into the atmosphere. Agricultural, environmental, and climatic shifts can alter CH4 sink profiles of soils, likely through shifts in CH4-assimilating microbial community structure and function. Landuse change, as forest and grassland ecosystems altered to agro-ecosystems, has already attenuated the soil CH4 sink potential, and are expected to be continued in the future. We hypothesized that variations in CH4 uptake rates in soils under different landuse practices could be an indicative of alterations in the abundance and/or type of methanotrophic communities in such soils. However, only a few studies have addressed to number and methanotrophs diversity and their correlation with the CH4 sink potential in soils of rehabilitated/restored lands. We focus on landuse practices that can potentially mitigate CH4 gas emissions, the most prominent of which are improved cropland, grazing land management, use of bio-fertilizers, and restoration of degraded lands. In this perspective paper, it is proposed that restoration of degraded lands can contribute considerably to improved soil CH4 sink strength by retrieving/conserving abundance and assortment of efficient methanotrophic communities. We believe that this report can assist in identifying future experimental directions to the relationships between landuse changes, methane-assimilating microbial communities and soil CH4 sinks. The exploitation of microbial communities other than methanotrophs can contribute significantly to the global CH4 sink potential and can add value in mitigating the CH4 problems. PMID:27379053

Degraded Land Restoration in Reinstating CH4 Sink.

PubMed

Singh, Jay Shankar; Gupta, Vijai K

2016-01-01

Methane (CH4), a potent greenhouse gas, contributes about one third to the global green house gas emissions. CH4-assimilating microbes (mostly methanotrophs) in upland soils play very crucial role in mitigating the CH4 release into the atmosphere. Agricultural, environmental, and climatic shifts can alter CH4 sink profiles of soils, likely through shifts in CH4-assimilating microbial community structure and function. Landuse change, as forest and grassland ecosystems altered to agro-ecosystems, has already attenuated the soil CH4 sink potential, and are expected to be continued in the future. We hypothesized that variations in CH4 uptake rates in soils under different landuse practices could be an indicative of alterations in the abundance and/or type of methanotrophic communities in such soils. However, only a few studies have addressed to number and methanotrophs diversity and their correlation with the CH4 sink potential in soils of rehabilitated/restored lands. We focus on landuse practices that can potentially mitigate CH4 gas emissions, the most prominent of which are improved cropland, grazing land management, use of bio-fertilizers, and restoration of degraded lands. In this perspective paper, it is proposed that restoration of degraded lands can contribute considerably to improved soil CH4 sink strength by retrieving/conserving abundance and assortment of efficient methanotrophic communities. We believe that this report can assist in identifying future experimental directions to the relationships between landuse changes, methane-assimilating microbial communities and soil CH4 sinks. The exploitation of microbial communities other than methanotrophs can contribute significantly to the global CH4 sink potential and can add value in mitigating the CH4 problems.

Constraining the sources of CH4 emissions during past abrupt climate change using CH4 triple isotopes mass balance from the ice core records

NASA Astrophysics Data System (ADS)

Dyonisius, M.; Petrenko, V. V.; Smith, A. W.; Hmiel, B.; Beck, J.; Seth, B.; Bock, M.; Hua, Q.; Yang, B.; Harth, C. M.; Beaudette, R.; Lee, J.; Erhardt, T.; Schmitt, J.; Brook, E.; Weiss, R. F.; Fischer, H.; Severinghaus, J. P.

2017-12-01

Methane (CH4) is the third most important greenhouse gas in the atmosphere after water vapor and CO2. Understanding how the natural CH4 budget has changed in response to changing climate in the past can provide insights on the sensitivity of the natural CH4 emissions to the current anthropogenic warming. CH4 isotopes (Δ14CH4, δ13C-CH4, and δD-CH4) from ice cores can be used to fingerprint the sources of CH4 increases in the past. We have successfully extracted 6 large volume (>1000kg) ice core samples from Taylor Glacier, Antarctica spanning the Oldest Dryas-Bølling transition ( 14.7ka) - the first abrupt warming and CH4 rise since the Last Glacial Maximum. Among the CH4 isotopes, our Δ 14CH4 data are unique in their ability to unambiguously distinguish between "old" CH4 sources (e.g. marine clathrate, geologic sources, old permafrost) and "modern" CH4 sources (e.g. tropical and boreal wetlands). Our Δ14CH4 data unambiguously rule out marine clathrate and old permafrost as the sources of the abrupt CH4 rise. Preliminary CH4 stable isotopes box modeling combined with interpolar CH4 concentration gradient from existing ice core records suggest that tropical wetlands were the dominant driver for the Oldest Dryas-Bølling CH4 rise.

A Mechanistical Study on the Formation of Dimethyl Ether (CH3OCH3) and Ethanol (CH3CH2OH) in Methanol-containing Ices and Implications for the Chemistry of Star-forming Regions

NASA Astrophysics Data System (ADS)

Bergantini, Alexandre; Góbi, Sándor; Abplanalp, Matthew J.; Kaiser, Ralf I.

2018-01-01

The underlying formation mechanisms of complex organic molecules (COMs)—in particular, structural isomers—in the interstellar medium (ISM) are largely elusive. Here, we report new experimental findings on the role of methanol (CH3OH) and methane (CH4) ices in the synthesis of two C2H6O isomers upon interaction with ionizing radiation: ethanol (CH3CH2OH) and dimethyl ether (CH3OCH3). The present study reproduces the interstellar abundance ratios of both species with ethanol to dimethyl ether branching ratios of (2.33 ± 0.14):1 suggesting that methanol and methane represents the key precursor to both isomers within interstellar ices. Exploiting isotopic labeling combined with reflectron time-of-flight mass spectrometry (Re-TOF-MS) after isomer selective vacuum ultra-violet (VUV) photoionization of the neutral molecules, we also determine the formation mechanisms of both isomers via radical–radical recombination versus carbene (CH2) insertion with the former pathway being predominant. Formation routes to higher molecular weight reaction products such as ethylene glycol (HOCH2CH2OH), dimethyl peroxide (CH3OOCH3), and methoxymethanol (CH3OCH2OH) are discussed briefly as well.

omega-Amino acid:pyruvate transaminase from Alcaligenes denitrificans Y2k-2: a new catalyst for kinetic resolution of beta-amino acids and amines.

PubMed

Yun, Hyungdon; Lim, Seongyop; Cho, Byung-Kwan; Kim, Byung-Gee

2004-04-01

Alcaligenes denitrificans Y2k-2 was obtained by selective enrichment followed by screening from soil samples, which showed omega-amino acid:pyruvate transaminase activity, to kinetically resolve aliphatic beta-amino acid, and the corresponding structural gene (aptA) was cloned. The gene was functionally expressed in Escherichia coli BL21 by using an isopropyl-beta-D-thiogalactopyranoside (IPTG)-inducible pET expression system (9.6 U/mg), and the recombinant AptA was purified to show a specific activity of 77.2 U/mg for L-beta-amino-n-butyric acid (L-beta-ABA). The enzyme converts various beta-amino acids and amines to the corresponding beta-keto acids and ketones by using pyruvate as an amine acceptor. The apparent K(m) and V(max) for L-beta-ABA were 56 mM and 500 U/mg, respectively, in the presence of 10 mM pyruvate. In the presence of 10 mM L-beta-ABA, the apparent K(m) and V(max) for pyruvate were 11 mM and 370 U/mg, respectively. The enzyme exhibits high stereoselectivity (E > 80) in the kinetic resolution of 50 mM D,L-beta-ABA, producing optically pure D-beta-ABA (99% enantiomeric excess) with 53% conversion.

ω-Amino Acid:Pyruvate Transaminase from Alcaligenes denitrificans Y2k-2: a New Catalyst for Kinetic Resolution of β-Amino Acids and Amines

PubMed Central

Yun, Hyungdon; Lim, Seongyop; Cho, Byung-Kwan; Kim, Byung-Gee

2004-01-01

Alcaligenes denitrificans Y2k-2 was obtained by selective enrichment followed by screening from soil samples, which showed ω-amino acid:pyruvate transaminase activity, to kinetically resolve aliphatic β-amino acid, and the corresponding structural gene (aptA) was cloned. The gene was functionally expressed in Escherichia coli BL21 by using an isopropyl-β-d-thiogalactopyranoside (IPTG)-inducible pET expression system (9.6 U/mg), and the recombinant AptA was purified to show a specific activity of 77.2 U/mg for l-β-amino-n-butyric acid (l-β-ABA). The enzyme converts various β-amino acids and amines to the corresponding β-keto acids and ketones by using pyruvate as an amine acceptor. The apparent Km and Vmax for l-β-ABA were 56 mM and 500 U/mg, respectively, in the presence of 10 mM pyruvate. In the presence of 10 mM l-β-ABA, the apparent Km and Vmax for pyruvate were 11 mM and 370 U/mg, respectively. The enzyme exhibits high stereoselectivity (E > 80) in the kinetic resolution of 50 mM d,l-β-ABA, producing optically pure d-β-ABA (99% enantiomeric excess) with 53% conversion. PMID:15066855

Inverse Modeling of Surface CH4 and δ13C-CH4 Measurements to Understand Recent Trends in Global Methane Emissions

NASA Astrophysics Data System (ADS)

Karmakar, S.; Butenhoff, C. L.; Rice, A. L.; Lofdahl, D. B.; Khalil, A. K.

2016-12-01

Methane (CH4) is the second most important greenhouse gas with a radiative forcing of 0.97 W/m2 including both direct and indirect effects and a global warming potential of 28 over a 100-year time horizon. Unlike CO2 whose rate of growth in the atmosphere has remained positive and increased in recent decades, the behavior of atmospheric methane is considerably more complex and is much less understood on account of the spatiotemporal variability of its emissions which include biogenic (e.g. wetlands, ruminants, rice agriculture), thermogenic (fossil fuels), and pyrogenic (i.e. biomass burning) sources. After sustained growth during most of the 20th century, the CH4 growth rate declined falling from 15 ppbv/yr during the 1980s to 6 ppbv/yr in the 1990s to near-zero and even negative values in the early 2000s. With some surprise however, the growth rate rebounded in 2007 and has been on average 6 ppbv/yr during the past 10 years. During this same period the 13CH4/12CH4 ratio of atmospheric CH4 also declined suggesting the recent CH4 growth was caused by an increase in 13CH4-depleted biogenic emissions. Here, we provide additional insight into the recent behavior of atmospheric methane by performing a global three-dimensional Bayesian inversion of surface CH4 and 13CH4/12CH4 ratios over the period 1985-2015 using NOAA Global Monitoring Division (GMD) CH4 measurements and the GEOS-Chem chemical-transport model (CTM) at a horizontal grid resolution of 2ox2.5o. The use of the 3-D model allows us to exploit spatial patterns in the global CH4 and 13CH4/12CH4 fields that provide additional constraints on the retrieval of the time-dependent CH4 fluxes. This work follows up on our previous CH4 inversion where we used a 4ox5o horizontal grid for GEOS-Chem to retrieve fluxes from 1985 to 2009. At higher resolution more information is extracted from the observations due to improved model skill and a smaller number of stations aggregated within model grid cells. This increases the

Thermal decomposition and oxidation of CH3OH.

PubMed

Lee, Pei-Fang; Matsui, Hiroyuki; Xu, Ding-Wei; Wang, Niann-Shiah

2013-01-24

Thermal decomposition of CH(3)OH diluted in Ar has been studied by monitoring H atoms behind reflected shock waves of 100 ppm CH(3)OH + Ar. The total decomposition rate k(1) for CH(3)OH + M → products obtained in this study is expressed as, ln(k(1)/cm(3) molecule(-1) s(-1)) = -(14.81 ± 1.22) - (38.86 ± 1.82) × 10(3)/T, over 1359-1644 K. The present result on k(1) is indicated to be substantially smaller than the extrapolation of the most of the previous experimental data but consistent with the published theoretical results [Faraday Discuss. 2002, 119, 191-205 and J. Phys. Chem. A 2007, 111, 3932-3950]. Oxidation of CH(3)OH has been studied also by monitoring H atoms behind shock waves of (0.35-100) ppm CH(3)OH + (100-400) ppm O(2) + Ar. For the low concentration CH(3)OH (below 10 ppm) + O(2) mixtures, the initial concentration of CH(3)OH is evaluated by comparing evolutions of H atoms in the same concentration of CH(3)OH with addition of 300 ppm H(2) diluted in Ar. The branching fraction for CH(3)OH + Ar → (1)CH(2) + H(2)O + Ar has been quantitatively evaluated from this comparative measurements with using recent experimental result on the yield of H atoms in the reaction of (1,3)CH(2) + O(2) [J. Phys. Chem. A 2012, 116, 9245-9254]; i.e., the branching fraction for the above reaction is evaluated as, φ(1a) = 0.20 ± 0.04 at T = 1880-2050 K, in the 1.3 and 3.5 ppm CH(3)OH + 100 ppm O(2) samples. An extended reaction mechanism for the pyrolysis and oxidation of CH(3)OH is constructed based on the results of the present study combined with the oxidation mechanism of natural gas [GRI-Mech 3.0]; evolution of H atoms can be predicted very well with this new reaction scheme over a wide concentration range for the pyrolysis (0.36-100 ppm CH(3)OH), and oxidation (0.36-100 ppm CH(3)OH + 100/400 ppm O(2)) of methanol.

Subsoil methanogenesis as source of stem CH4 emission in upland forest trees: preferential CH4 transport via the root system?

NASA Astrophysics Data System (ADS)

Maier, M.; Machacova, K.; Urban, O.; Friederike, L.

2016-12-01

Quantifying and understanding green house gas fluxes in natural soil-plant-atmosphere systems are crucial to predicting global climate change. Wetland species or trees at waterlogged sites are known to emit large amounts of CH4. Yet upland forest soils are regarded as CH4 sinks and tree species like upland European beech (Fagus sylvatica, L.) are assumed not to emit CH4. We studied the soil-atmosphere and stem-atmosphere fluxes of CH4, and soil gas profiles at two upland beech forest sites in Central Europe. Soil was a net CH4 sink at both. Unusually there was one beech tree with substantial CH4 emissions that were higher than the CH4 sink of the soil. The soil gas profile at this tree indicated CH4 production at a soil depth >0.3 m, despite the net uptake of CH4 observed at the soil surface adjacent to the tree. Field soil assessment showed strong redoximorphic color patterns in the adjacent soil. We think that there is a transport link between the soil and stem via the root system representing a preferential transport mechanism for CH4 despite the fact that beech roots usually do not bear aerenchyma. The gas transport process , either via dissolved CH4 in the xylem water or in the root gas phase, is not yet clear. The observed CH4 stem emissions represent an important CH4flux in this ecosystem, und thus should be considered in future research. AcknowledgementThis research was financially supported by the Czech Academy of Sciences and the German Academic Exchange Service within the project "Methane (CH4) and nitrous oxide (N2O) emissions from Fagus sylvatica trees" (DAAD-15-03), National Programme for Sustainability I (LO1415) and project DFG (MA 5826/2-1). We would like to thank Marek Jakubik, Katerina Svobodova, Sinikka Paulus, Ellen Halaburt and Sally Haddad for technical support.

Direct formation of (CH sub 3 ) sub 2 HSiCl from silicon and CH sub 3 Cl

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

Magrini, K.A.; Falconer, J.L.; Koel, B.E.

1989-07-13

A Cu-catalyzed reaction procedure was found for the selective formation of dimethylchlorosilane ((CH{sub 3}){sub 2}HSiCl) from the direct reaction of CH{sub 3}Cl with solid Si. The new procedure is a two-step process. A Cu/Si sample is prepared by evaporating Cu onto clean polycrystalline Si under ultrahigh vacuum, and the Cu/Si surface is first activated by exposure to 10% HSiCl{sub 3}/CH{sub 3}Cl at 598 K. After the HSiCl{sub 3}CH{sub 3}Cl mixture is evacuated from the reactor, the activated Cu/Si surface is reacted in fresh CH{sub 3}Cl. For low surface concentrations of Cu, the partially hydrogenated silane, (CH{sub 3}){sub 2}HSiCl, is selectivelymore » produced. Trichlorosilane was also found to activate polycrystalline Si (in the absence of Cu) for production of highly chlorinated methylchlorosilanes at a much higher rate than on the Cu/Si surface but with poor selectively to (CH{sub 3}){sub 2}HSiCl. All reactions are carried out at atmospheric pressure in a reactor that is attached to an ultrahigh-vacuum chamber. This allows surface analysis of Auger electron spectroscopy, which detected SiCl{sub x} on reacted surfaces. These SiCl{sub x} sites, which appear necessary for methylchlorosilane formation, are apparently formed during activation by HSiCl{sub 3}.« less

Photodissociation of the CH3O and CH3S radical molecules: An ab initio electronic structure study

PubMed Central

Bouallagui, A.; Zanchet, A.; Yazidi, O.; Jaïdane, N.; Bañares, L.; Senent, M.L.; García-Vela, A.

2018-01-01

The electronic states and the spin-orbit couplings between them involved in the photodissociation process of the radical molecules CH3X, CH3X → CH3 + X(X = O, S), taking place after the Ā(2A1) ← X̄(2E) transition, have been investigated using highly correlated ab initio techniques. A two-dimensional representation of both the potential-energy surfaces (PESs) and the couplings is generated. This description includes the C-X dissociative mode and the CH3 umbrella mode. Spin-orbit effects are found to play a relevant role on the shape of the excited state potential-energy surfaces, particularly in the CH3S case where the spin-orbit couplings are more than twice more intense than in CH3O. The potential surfaces and couplings reported here for the present set of electronic states allow for the first complete description of the above photodissociation process. The different photodissociation mechanisms are analyzed and discussed in the light of the results obtained. PMID:29143005

A DFT-Elucidated Comparison of the Solution-Phase and SAM Electrochemical Properties of Short-Chain Mercaptoalkylferrocenes: Synthetic and Spectroscopic Aspects, and the Structure of Fc-CH2CH2-S-S-CH2CH2-Fc.

PubMed

Lewtak, Jan P; Landman, Marilé; Fernández, Israel; Swarts, Jannie C

2016-03-07

Facile synthetic procedures to synthesize a series of difficult-to-obtain mercaptoalkylferrocenes, namely, Fc(CH2)nSH, where n = 1 (1), 2 (2), 3 (3), or 4 (4) and Fc = Fe(η(5)-C5H5)(η(5)-C5H4), are reported. Dimerization of 1-4 to the corresponding disulfides 19-22 was observed in air. Dimer 20 (Z = 2) crystallized in the triclinic space group P1̅. Dimers 20-22 could be reduced back to the original Fc(CH2)nSH derivatives with LiAlH4 in refluxing tetrahydrofuran. Density functional theory (DFT) calculations showed that the highest occupied molecular orbital of 1-4 lies exclusively on the ferrocenyl group implying that the electrochemical oxidation observed at ca. -15 < Epa < 76 mV versus FcH/FcH(+) involves exclusively an Fe(II) to Fe(III) process. Further DFT calculations showed this one-electron oxidation is followed by proton loss on the thiol group to generate a radical, Fc(CH2)nS(•), with spin density mainly located on the sulfur. Rapid exothermic dimerization leads to the observed dimers, Fc(CH2)n-S-S-(CH 2)nFc. Reduction of the ferrocenium groups on the dimer occurs at potentials that still showed the ferrocenyl group ΔE = Epa,monomer - Epc,dimer ≤ 78 mV, indicating that the redox properties of the ferrocenyl group on the mercaptans are very similar to those of the dimer. (1)H NMR measurements showed that, like ferrocenyl oxidation, the resonance position of the sulfhydryl proton, SH, and others, are dependent on -(CH2)n- chain length. Self-assembled monolayers (SAMs) on gold were generated to investigate the electrochemical behavior of 1-4 in the absence of diffusion. Under these conditions, ΔE approached 0 mV for the longer chain derivatives at slow scan rates. The surface-bound ferrocenyl group of the metal-thioether, Fc(CH2)n -S-Au, is oxidized at approximately equal potentials as the equivalent CH2Cl2-dissolved ferrocenyl species 1-4. Surface coverage by the SAMs is dependent on alkyl chain length with the largest coverage obtained for 4, while

Infrared spectroscopy of solid normal hydrogen doped with CH3F and O2 at 4.2 K: CH3F:O2 complex and CH3F migration

NASA Astrophysics Data System (ADS)

Abouaf-Marguin, L.; Vasserot, A.-M.

2011-04-01

Double doping of solid normal hydrogen with CH3F and O2 at about 4.2 K gives evidence of (ortho-H2)n:CH3F clusters and of O2:CH3F complex formation. FTIR analysis of the time evolution of the spectra in the region of the v3 C-F stretching mode indicates that these clusters behave very differently from (ortho-H2)n:H2O clusters. The main point is the observed migration of CH3F molecules in solid para-H2 at 4.2 K which differs from that of H2O under identical experimental conditions. This is confirmed by an increase over time of the integrated intensity of the CH3F:O2 complex with a rate constant K = 2.7(2) . 10-4 s-1.

InChIKey collision resistance: an experimental testing

PubMed Central

2012-01-01

InChIKey is a 27-character compacted (hashed) version of InChI which is intended for Internet and database searching/indexing and is based on an SHA-256 hash of the InChI character string. The first block of InChIKey encodes molecular skeleton while the second block represents various kinds of isomerism (stereo, tautomeric, etc.). InChIKey is designed to be a nearly unique substitute for the parent InChI. However, a single InChIKey may occasionally map to two or more InChI strings (collision). The appearance of collision itself does not compromise the signature as collision-free hashing is impossible; the only viable approach is to set and keep a reasonable level of collision resistance which is sufficient for typical applications. We tested, in computational experiments, how well the real-life InChIKey collision resistance corresponds to the theoretical estimates expected by design. For this purpose, we analyzed the statistical characteristics of InChIKey for datasets of variable size in comparison to the theoretical statistical frequencies. For the relatively short second block, an exhaustive direct testing was performed. We computed and compared to theory the numbers of collisions for the stereoisomers of Spongistatin I (using the whole set of 67,108,864 isomers and its subsets). For the longer first block, we generated, using custom-made software, InChIKeys for more than 3 × 1010 chemical structures. The statistical behavior of this block was tested by comparison of experimental and theoretical frequencies for the various four-letter sequences which may appear in the first block body. From the results of our computational experiments we conclude that the observed characteristics of InChIKey collision resistance are in good agreement with theoretical expectations. PMID:23256896

InChIKey collision resistance: an experimental testing.

PubMed

Pletnev, Igor; Erin, Andrey; McNaught, Alan; Blinov, Kirill; Tchekhovskoi, Dmitrii; Heller, Steve

2012-12-20

InChIKey is a 27-character compacted (hashed) version of InChI which is intended for Internet and database searching/indexing and is based on an SHA-256 hash of the InChI character string. The first block of InChIKey encodes molecular skeleton while the second block represents various kinds of isomerism (stereo, tautomeric, etc.). InChIKey is designed to be a nearly unique substitute for the parent InChI. However, a single InChIKey may occasionally map to two or more InChI strings (collision). The appearance of collision itself does not compromise the signature as collision-free hashing is impossible; the only viable approach is to set and keep a reasonable level of collision resistance which is sufficient for typical applications.We tested, in computational experiments, how well the real-life InChIKey collision resistance corresponds to the theoretical estimates expected by design. For this purpose, we analyzed the statistical characteristics of InChIKey for datasets of variable size in comparison to the theoretical statistical frequencies. For the relatively short second block, an exhaustive direct testing was performed. We computed and compared to theory the numbers of collisions for the stereoisomers of Spongistatin I (using the whole set of 67,108,864 isomers and its subsets). For the longer first block, we generated, using custom-made software, InChIKeys for more than 3 × 1010 chemical structures. The statistical behavior of this block was tested by comparison of experimental and theoretical frequencies for the various four-letter sequences which may appear in the first block body.From the results of our computational experiments we conclude that the observed characteristics of InChIKey collision resistance are in good agreement with theoretical expectations.

High Resolution CH4 Emissions and Dissolved CH4 Measurements Elucidate Surface Gas Exchange Processes in Toolik Lake, Arctic Alaska

NASA Astrophysics Data System (ADS)

Del Sontro, T.; Sollberger, S.; Kling, G. W.; Shaver, G. R.; Eugster, W.

2013-12-01

Approximately 14% of the Alaskan North Slope is covered in lakes of various sizes and depths. Diffusive carbon emissions (CH4 and CO2) from these lakes offset the tundra sink by ~20 %, but the offset would substantially increase if ebullitive CH4 emissions were also considered. Ultimately, arctic lake CH4 emissions are not insignificant in the global CH4 budget and their contribution is bound to increase due to impacts from climate change. Here we present high resolution CH4 emission data as measured via eddy covariance and a Los Gatos gas analyzer during the ice free period from Toolik Lake, a deep (20 m) Arctic lake located on the Alaskan North Slope, over the last few summers. Emissions are relatively low (< 25 mg CH4 m-2 d-1) with little variation over the summer. Diurnal variations regularly occur, however, with up to 3 times higher fluxes at night. Gas exchange is a relatively difficult process to estimate, but is normally done so as the product of the CH4 gradient across the air-water interface and the gas transfer velocity, k. Typically, k is determined based on the turbulence on the water side of the interface, which is most commonly approximated by wind speed; however, it has become increasingly apparent that this assumption does not remain valid across all water bodies. Dissolved CH4 profiles in Toolik revealed a subsurface peak in CH4 at the thermocline of up to 3 times as much CH4 as in the surface water. We hypothesize that convective mixing at night due to cooling surface waters brings the subsurface CH4 to the surface and causes the higher night fluxes. In addition to high resolution flux emission estimates, we also acquired high resolution data for dissolved CH4 in surface waters of Toolik Lake during the last two summers using a CH4 equilibrator system connected to a Los Gatos gas analyzer. Thus, having both the flux and the CH4 gradient across the air-water interface measured directly, we can calculate k and investigate the processes influencing

The Student Mix Software System (SMSS)

DTIC Science & Technology

1986-04-01

CH $ LOCATE 22,16: IF CH $ = &#34C&#34 IF CH $ = &#34c&#34 IF CH $ = &#34X&#34 IF CH ...LOCATE LOCATE LOCATE LOCATE IF FLAG = 1 INPUT CH $ LOCATE 22,16 𔃾) ARI STUDENTS DO NOT CHANGE SEMINARS: 7,73: PRINT RULE$(4);; LOCATE 8,10...CHOICE: RETURN THE THE P) PERFERED, DEFAULTS" PREVIOUS MENU, D) DON’T CARE&#34 IF IF IF IF CH $ CH ? CH ? CH ? PRINT &#34 THEN GOTO 130 5

The DFT Calculations of Structures and EPR Parameters for the Dinuclear Paddle-Wheel Copper(II) Complex {Cu2(μ2-O2CCH3)4}(OCNH2CH3) as Powder or Single Crystal

NASA Astrophysics Data System (ADS)

Ding, Chang-Chun; Wu, Shao-Yi; Xu, Yong-Qiang; Zhang, Li-Juan; Zhang, Zhi-Hong; Zhu, Qin-Sheng; Wu, Ming-He; Teng, Bao-Hua

2017-10-01

Density functional theory (DFT) calculations of the structures and the Cu2+ g factors (gx, gy and gz ) and hyperfine coupling tensor A (Ax , Ay and Az ) were performed for the paddle-wheel (PW)-type binuclear copper(II) complex {Cu2(μ2-O2CCH3)4}(OCNH2CH3) powder and single crystal. Calculations were carried out with the ORCA software using the functionals BHandHlyp, B3P86 and B3LYP with five different basis sets: 6-311g, 6-311g(d,p), VTZ, def-2 and def2-TZVP. Results were tested by the MPAD analysis to find the most suitable functional and basis sets. The electronic structure and covalency between copper and oxygen were investigated by the electron localisation function and the localised orbital locator as well as the Mayer bond order for the [CuO5] group. The optical spectra were theoretically calculated by the time-dependent DFT module and plotted by the Multiwfn program for the [CuO5] group and reasonably associated with the local structure in the vicinity of the central ion copper. In addition, the interactions between the OCNH2CH3, NH3 and H2O molecules and the uncoordinated PW copper(II) complex were studied, and the corresponding adsorption energies, the frequency shifts with respect to the free molecules and the changes of the Cu-Cu distances were calculated and compared with the relevant systems.

Background CH4 and N2O fluxes in low-input short rotation coppice

NASA Astrophysics Data System (ADS)

Görres, Carolyn-Monika; Zenone, Terenzio; Ceulemans, Reinhart

2016-04-01

Extensively managed short rotation coppice systems are characterized by low fluxes of CH4 and N2O. However due to the large global warming potential of these trace gases (GWP100: CH4: 34, N2O: 298), such background fluxes can still significantly contribute to offsetting the CO2 uptake of short rotation coppice systems. Recent technological advances in fast-response CH4 and N2O analysers have improved our capability to capture these background fluxes, but their quantification still remains a challenge. As an example, we present here CH4 and N2O fluxes from a short-rotation bioenergy plantation in Belgium. Poplars have been planted in a double-row system on a loamy sand in 2010 and coppiced in the beginning of 2012 and 2014 (two-year rotation system). In 2013 (June - November) and 2014 (April - August), the plantation's CH4 and N2O fluxes were measured in parallel with an eddy covariance tower (EC) and an automated chamber system (AC). The EC had a detection limit of 13.68 and 0.76 μmol m-2 h-1 for CH4 and N2O, respectively. The median detection limit of the AC was 0.38 and 0.08 μmol m-2 h-1 for CH4 and N2O, respectively. The EC picked up a few high CH4 emission events with daily averages >100 μmol m-2 h-1, but a large proportion of the measured fluxes were within the EC's detection limit. The same was true for the EC-derived N2O fluxes where the daily average flux was often close to the detection limit. Sporadically, some negative (uptake) fluxes of N2O were observed. On the basis of the EC data, no clear link was found between CH4 and N2O fluxes and environmental variables. The problem with fluxes within the EC detection limit is that a significant amount of the values can show the opposite sign, thus "mirroring" the true flux. Subsequently, environmental controls of background trace gas fluxes might be disguised in the analysis. As a next step, it will be tested if potential environmental drivers of background CH4 and N2O fluxes at the plantation can be

Effects of elevated ozone concentration on CH4 and N2O emission from paddy soil under fully open-air field conditions.

PubMed

Tang, Haoye; Liu, Gang; Zhu, Jianguo; Kobayashi, Kazuhiko

2015-04-01

We investigated the effects of elevated ozone concentration (E-O3) on CH4 and N2O emission from paddies with two rice cultivars: an inbred Indica cultivar Yangdao 6 (YD6) and a hybrid one II-you 084 (IIY084), under fully open-air field conditions in China. A mean 26.7% enhancement of ozone concentration above the ambient level (A-O3) significantly reduced CH4 emission at tillering and flowering stages leading to a reduction of seasonal integral CH4 emission by 29.6% on average across the two cultivars. The reduced CH4 emission is associated with O3-induced reduction in the whole-plant biomass (-13.2%), root biomass (-34.7%), and maximum tiller number (-10.3%), all of which curbed the carbon supply for belowground CH4 production and its release from submerged soil to atmosphere. Although no significant difference was detected between the cultivars in the CH4 emission response to E-O3, a larger decrease in CH4 emission with IIY084 (-33.2%) than that with YD6 (-7.0%) was observed at tillering stage, which may be due to the larger reduction in tiller number in IIY084 by E-O3. Additionally, E-O3 reduced seasonal mean NOx flux by 5.7% and 11.8% with IIY084 and YD6, respectively, but the effects were not significant statistically. We found that the relative response of CH4 emission to E-O3 was not significantly different from those reported in open-top chamber experiments. This study has thus confirmed that increasing ozone concentration would mitigate the global warming potential of CH4 and suggested consideration of the feedback mechanism between ozone and its precursor emission into the projection of future ozone effects on terrestrial ecosystem. © 2014 John Wiley & Sons Ltd.

Efficacy of polysaccharide from Alcaligenes xylosoxidans MSA3 administration as protection against γ-radiation in female rats

PubMed Central

Hassan, Amal I.; Ghoneim, Mona A. M.; Mahmoud, Manal G.; Asker, Mohsen M. S.; Mohamed, Saher S.

2016-01-01

Damage to normal tissues is a consequence of both therapeutic and accidental exposures to ionizing radiation. A water-soluble heteropolysaccharide called AXEPS, composed of glucose, galactose, rhamnose and glucouronic acid in a molar ratio of nearly 1.0:1.6:0.4:2.3, respectively, was isolated from culture medium of strain Alcaligenes xylosoxidans MSA3 by ethanol precipitation followed by freeze-drying. Chemical analysis, Fourier-transform infrared (FTIR) and chromatographic studies revealed that the molecular weight was 1.6 × 104 g mol−1. This study was designed to investigate the radioprotective and biological effects of AXEPS in alleviating the toxicity of ionizing radiation in female albino rats. A total of 32 female albino rats were divided into four groups. In the control group, rats were administered vehicle by tube for four weeks. The second group was administered AXEPS (100 mg/kg) orally by gavage for four weeks. Animals in the third group were exposed to whole-body γ-rays (5 Gy) and remained for 2 weeks without treatment. The fourth group received AXEPS (100 mg/kg) orally by gavage for two weeks before being exposed to whole-body γ-rays (5 Gy), then 24 h post γ-rays, they received AXEPS (100 mg/kg) in a treatment continuing till the end of the experiment (15 days after the whole–body γ-irradiation). Oral administration of AXEPS (100 mg/kg) significantly reversed the oxidative stress effects of radiation, as evidenced by the decrease in DNA damage in the bone marrow. Assessment of apoptosis and cell proliferation markers revealed that caspase-3 significantly increased in the irradiated group. Moreover, a significant decrease in the hematological constituents of peripheral blood, the chemotactic index and CD8+ T cells were observed in animals in the irradiation-only group, whereas an increase in the lymphocyte index was observed in animals in that group. In contrast, AXEPS treatment prevented these alterations. From our results, we conclude that

Global Inverse Modeling of CH4 and δ13C-CH4 Measurements to Understand Recent Trends in Methane Emissions

NASA Astrophysics Data System (ADS)

Karmakar, S.; Butenhoff, C. L.; Rice, A. L.; Khalil, A. K.

2017-12-01

Methane (CH4) is the second most important greenhouse gas with a radiative forcing of 0.97 W/m2 including both direct and indirect effects and a global warming potential of 28 over a 100-year time horizon. After a decades-long period of decline beginning in the 1980s, the methane growth rate rebounded in 2007 for reasons that are of current debate. During this same growth period atmospheric methane became less enriched in the 13CH4 isotope suggesting the recent CH4 growth was caused by an increase in 13CH4-depleted biogenic emissions. Recent papers have attributed this growth to increasing emissions from wetlands, rice agriculture, and ruminants. In this work we provide additional insight into the recent behavior of atmospheric methane and global wetland emissions by performing a three-dimensional Bayesian inversion of surface CH4 and 13CH4/12CH4 ratios using NOAA Global Monitoring Division (GMD) "event-level" CH4 measurements and the GEOS-Chem chemical-transport model (CTM) at a horizontal grid resolution of 2ox2.5o. The spatial pattern of wetland emissions was prescribed using soil moisture and temperature from GEOS-5 meteorology fields and soil carbon pools from the Lund-Potsdam-Jena global vegetation model. In order to reduce the aggregation error caused by a potentially flawed distribution and to account for isotopic measurements that indicate northern high latitude wetlands are isotopically depleted in 13CH4 relative to tropical wetlands we separated our pattern into three latitudinal bands (90-30°N, 30°N-0, 0-90°S). Our preliminary results support previous claims that the recent increase in atmospheric methane is driven by increases in biogenic CH4 emissions. We find that while wetland emissions from northern high latitudes (90-30°N) remained relatively constant during this time, southern hemisphere wetland emissions rebounded from a decade-long decline and began to rise again in 2007 and have remained elevated to the present. Emissions from rice

ChIP-nexus: a novel ChIP-exo protocol for improved detection of in vivo transcription factor binding footprints

PubMed Central

He, Qiye; Johnston, Jeff; Zeitlinger, Julia

2014-01-01

Understanding how eukaryotic enhancers are bound and regulated by specific combinations of transcription factors is still a major challenge. To better map transcription factor binding genome-wide at nucleotide resolution in vivo, we have developed a robust ChIP-exo protocol called ChIP experiments with nucleotide resolution through exonuclease, unique barcode and single ligation (ChIP-nexus), which utilizes an efficient DNA self-circularization step during library preparation. Application of ChIP-nexus to four proteins—human TBP and Drosophila NFkB, Twist and Max— demonstrates that it outperforms existing ChIP protocols in resolution and specificity, pinpoints relevant binding sites within enhancers containing multiple binding motifs and allows the analysis of in vivo binding specificities. Notably, we show that Max frequently interacts with DNA sequences next to its motif, and that this binding pattern correlates with local DNA sequence features such as DNA shape. ChIP-nexus will be broadly applicable to studying in vivo transcription factor binding specificity and its relationship to cis-regulatory changes in humans and model organisms. PMID:25751057

Additional Value of CH4 Measurement in a Combined 13C/H2 Lactose Malabsorption Breath Test: A Retrospective Analysis

PubMed Central

Houben, Els; De Preter, Vicky; Billen, Jaak; Van Ranst, Marc; Verbeke, Kristin

2015-01-01

The lactose hydrogen breath test is a commonly used, non-invasive method for the detection of lactose malabsorption and is based on an abnormal increase in breath hydrogen (H2) excretion after an oral dose of lactose. We use a combined 13C/H2 lactose breath test that measures breath 13CO2 as a measure of lactose digestion in addition to H2 and that has a better sensitivity and specificity than the standard test. The present retrospective study evaluated the results of 1051 13C/H2 lactose breath tests to assess the impact on the diagnostic accuracy of measuring breath CH4 in addition to H2 and 13CO2. Based on the 13C/H2 breath test, 314 patients were diagnosed with lactase deficiency, 138 with lactose malabsorption or small bowel bacterial overgrowth (SIBO), and 599 with normal lactose digestion. Additional measurement of CH4 further improved the accuracy of the test as 16% subjects with normal lactose digestion and no H2-excretion were found to excrete CH4. These subjects should have been classified as subjects with lactose malabsorption or SIBO. In conclusion, measuring CH4-concentrations has an added value to the 13C/H2 breath test to identify methanogenic subjects with lactose malabsorption or SIBO. PMID:26371034

Electron-spin-resonance studies of 12CH3F + , 13CH3F + , and 12CH2DF + in neon matrices at 4 K: Comparison with theoretical calculations

NASA Astrophysics Data System (ADS)

Knight, Lon B., Jr.; Gregory, Brian W.; Hill, Devon W.; Arrington, C. A.; Momose, Takamasa; Shida, Tadamasa

1991-01-01

Various isotopic forms of the methyl fluoride cation 12CH3F+, 13CH3F+, and 12CH2DF+ have been generated by photoionization at 16.8 eV and separately by electron bombardment at 50 eV. The first electron-spin-resonance (ESR) results are reported for this radical cation which was isolated in neon matrices at 4 K. The measured A tensors or nuclear hyperfine parameters were compared with the results obtained from various computational approaches. Surprising observations were the large amounts of spin density on the methyl group, especially the hydrogen atoms, and the extreme differences in the deuterated spectra compared to the nondeuterated case. The presence of a single D atom apparently acts to prevent dynamic Jahn-Teller averaging which makes the methyl hydrogens equivalent on the ESR time scale. Such a dramatic Jahn-Teller effect has been previously observed for the similar methane cations CH+4 and CH2D+2. The magnetic parameters for CH2DF+ in neon at 4 K are gX=2.0032(5), gY=2.0106(8), and gZ=2.0120(5); for H: AX = 483(1), AY=476(1), and AZ=483(1) MHz; for D: ‖AX‖=5.0(3), ‖AY‖<3, and ‖AZ‖=7.1(3) MHz; for 19F : AX=965(1), AY=-130(2), and AZ=-166(1) MHz. For CH3F+, the g tensor and 19F A tensor were similar to those above but the H atoms were equivalent with values of AX=317(1), AY=323(2), and AZ=312 MHz.

Recent Developments in C-H Activation for Materials Science in the Center for Selective C-H Activation.

PubMed

Zhang, Junxiang; Kang, Lauren J; Parker, Timothy C; Blakey, Simon B; Luscombe, Christine K; Marder, Seth R

2018-04-16

Abstract : Organic electronics is a rapidly growing field driven in large part by the synthesis of ∏-conjugated molecules and polymers. Traditional aryl cross-coupling reactions such as the Stille and Suzuki have been used extensively in the synthesis of ∏-conjugated molecules and polymers, but the synthesis of intermediates necessary for traditional cross-couplings can include multiple steps with toxic and hazardous reagents. Direct arylation through C-H bond activation has the potential to reduce the number of steps and hazards while being more atom-economical. Within the Center for Selective C-H Functionalization (CCHF), we have been developing C-H activation methodology for the synthesis of ∏-conjugated materials of interest, including direct arylation of difficult-to-functionalize electron acceptor intermediates and living polymerization of ∏-conjugated polymers through C-H activation.

Calculations on the orientation of the CH fragment in Co 3(CO) 9(μ 3-CH): Implications for metal surfaces

NASA Astrophysics Data System (ADS)

DeKock, Roger L.; Fehlner, Thomas P.

1982-07-01

A series of molecular orbital calculations using the Fenske-Hall method have been carried out on Co 3(CO) 9(μ 3-CH), in which the orientation of the CH fragment is varied with respect to the triangular plane of the three Co atoms. The calculations show that the energy differences between the orbitals that are predominantly CH in character are affected very little by the orientation of the CH fragment. These calculated differences are Δ(2 σ-1 σ)≅7 eV and Δ(1 π-1 σ)≅ 10.5 eV. The calculated splitting of the degenerate 1π orbitals for geometries with tilted CH fragments never amounted to more than 0.46 eV. Mixing of CH orbitals into the predominantly Co 3d manifold was extensive in all of the calculations. These calculations provide no support for the interpretation of energy loss and photoemission electron spectroscopy experiments in terms of CH fragments that are tilted with respect to the metal surface, but such an interpretation cannot be eliminated due to the diffuse nature of the spectral bands in the photoemission experiments.

ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data.

PubMed

Wu, Song; Wang, Jianmin; Zhao, Wei; Pounds, Stanley; Cheng, Cheng

2010-06-03

ChIP-Seq is a powerful tool for identifying the interaction between genomic regulators and their bound DNAs, especially for locating transcription factor binding sites. However, high cost and high rate of false discovery of transcription factor binding sites identified from ChIP-Seq data significantly limit its application. Here we report a new algorithm, ChIP-PaM, for identifying transcription factor target regions in ChIP-Seq datasets. This algorithm makes full use of a protein-DNA binding pattern by capitalizing on three lines of evidence: 1) the tag count modelling at the peak position, 2) pattern matching of a specific tag count distribution, and 3) motif searching along the genome. A novel data-based two-step eFDR procedure is proposed to integrate the three lines of evidence to determine significantly enriched regions. Our algorithm requires no technical controls and efficiently discriminates falsely enriched regions from regions enriched by true transcription factor (TF) binding on the basis of ChIP-Seq data only. An analysis of real genomic data is presented to demonstrate our method. In a comparison with other existing methods, we found that our algorithm provides more accurate binding site discovery while maintaining comparable statistical power.

The ChArMEx database

NASA Astrophysics Data System (ADS)

Ferré, Hélène; Belmahfoud, Nizar; Boichard, Jean-Luc; Brissebrat, Guillaume; Cloché, Sophie; Descloitres, Jacques; Fleury, Laurence; Focsa, Loredana; Henriot, Nicolas; Mière, Arnaud; Ramage, Karim; Vermeulen, Anne; Boulanger, Damien

2015-04-01

The Chemistry-Aerosol Mediterranean Experiment (ChArMEx, http://charmex.lsce.ipsl.fr/) aims at a scientific assessment of the present and future state of the atmospheric environment in the Mediterranean Basin, and of its impacts on the regional climate, air quality, and marine biogeochemistry. The project includes long term monitoring of environmental parameters , intensive field campaigns, use of satellite data and modelling studies. Therefore ChARMEx scientists produce and need to access a wide diversity of data. In this context, the objective of the database task is to organize data management, distribution system and services, such as facilitating the exchange of information and stimulating the collaboration between researchers within the ChArMEx community, and beyond. The database relies on a strong collaboration between ICARE, IPSL and OMP data centers and has been set up in the framework of the Mediterranean Integrated Studies at Regional And Locals Scales (MISTRALS) program data portal. ChArMEx data, either produced or used by the project, are documented and accessible through the database website: http://mistrals.sedoo.fr/ChArMEx. The website offers the usual but user-friendly functionalities: data catalog, user registration procedure, search tool to select and access data... The metadata (data description) are standardized, and comply with international standards (ISO 19115-19139; INSPIRE European Directive; Global Change Master Directory Thesaurus). A Digital Object Identifier (DOI) assignement procedure allows to automatically register the datasets, in order to make them easier to access, cite, reuse and verify. At present, the ChArMEx database contains about 120 datasets, including more than 80 in situ datasets (2012, 2013 and 2014 summer campaigns, background monitoring station of Ersa...), 25 model output sets (dust model intercomparison, MEDCORDEX scenarios...), a high resolution emission inventory over the Mediterranean... Many in situ datasets

The CH/π hydrogen bond: Implication in chemistry

NASA Astrophysics Data System (ADS)

Nishio, M.

2012-06-01

The CH/π hydrogen bond is the weakest extreme of hydrogen bonds that occurs between a soft acid CH and a soft base π-system. Implication in chemistry of the CH/π hydrogen bond includes issues of conformation, crystal packing, and specificity in host/guest complexes. The result obtained by analyzing the Cambridge Structural Database is reviewed. The peculiar axial preference of isopropyl group in α-phellandrene and folded conformation of levopimaric acid have been explained in terms of the CH/π hydrogen bond, by high-level ab initio MO calculations. Implication of the CH/π hydrogen bond in structural biology is also discussed, briefly.

29 CFR 34.34 - Monitoring.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 29 Labor 1 2010-07-01 2010-07-01 true Monitoring. 34.34 Section 34.34 Labor Office of the... Nondiscrimination and Equal Opportunity Requirements of JTPA § 34.34 Monitoring. (a) The Director may periodically... monitoring directly any JTPA recipient or from investigating any matter necessary to determine a recipient's...

Induction of immune-related gene expression in Ctenopharyngodon idella kidney cells by secondary metabolites from immunostimulatory Alcaligenes faecalis FY-3.

PubMed

Wu, Z-F; Liu, G-L; Zhou, Z; Wang, G-X; Xia, L; Liu, J-L

2012-08-01

This study was undertaken to isolate active secondary metabolites from immunostimulatory Alcaligenes faecalis FY-3 and evaluate their activities using grass carp Ctenopharyngodon idella kidney (CIK) cells. By applying chromatography techniques and successive recrystallization, three purified metabolites were obtained and identified by spectral data (mass spectrometry and nuclear magnetic resonance) as: (1) phenylacetic acid, (2) p-hydroxyphenylacetylamide and (3) cyclo-(Gly-(L)-Pro). CIK cells were stimulated by different concentrations (1, 10 and 100 μg/ml) of the isolated compounds, and expression of MyD88, IL-1β, TNF-α, type I-IFN and IL-8 genes at different time points (2, 8 and 24 h) post-stimulation was quantified by real-time PCR. The known immunostimulatory agent lipopolysaccharide (LPS) was used as a positive control. To analyse whether these compounds are toxic to the cells, the methyl tetrazolium assay was employed to measure changes in cell viability. The obtained results revealed that transcribing level of MyD88, an important adaptor molecule in toll-like receptor signalling pathway, was augmented remarkably by all the three isolated compounds and LPS as early as 2-h exposure. These compounds also induced gene expression of cytokines such as IL-1β, TNF-α and type I-IFN. Under the experimental conditions, none of the test compounds is toxic to the CIK cells. These findings demonstrate that the immunostimulatory properties of the three metabolites [phenylacetic acid, p-hydroxyphenylacetylamide and cyclo-(Gly-(L)-Pro)] from A. faecalis FY-3 in CIK cells and highlight the potential of using these metabolites as immunostimulants in fish aquaculture. © 2012 The Authors. Scandinavian Journal of Immunology © 2012 Blackwell Publishing Ltd.

The products of the thermal decomposition of CH{sub 3}CHO

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

Vasiliou, AnGayle; National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, Colorado 80401; Piech, Krzysztof M.

2011-07-07

We have used a heated 2 cm x 1 mm SiC microtubular ({mu}tubular) reactor to decompose acetaldehyde: CH{sub 3}CHO +{Delta}{yields} products. Thermal decomposition is followed at pressures of 75-150 Torr and at temperatures up to 1675 K, conditions that correspond to residence times of roughly 50-100 {mu}s in the {mu}tubular reactor. The acetaldehyde decomposition products are identified by two independent techniques: vacuum ultraviolet photoionization mass spectroscopy (PIMS) and infrared (IR) absorption spectroscopy after isolation in a cryogenic matrix. Besides CH{sub 3}CHO, we have studied three isotopologues, CH{sub 3}CDO, CD{sub 3}CHO, and CD{sub 3}CDO. We have identified the thermal decomposition productsmore » CH{sub 3} (PIMS), CO (IR, PIMS), H (PIMS), H{sub 2} (PIMS), CH{sub 2}CO (IR, PIMS), CH{sub 2}=CHOH (IR, PIMS), H{sub 2}O (IR, PIMS), and HC{identical_to}CH (IR, PIMS). Plausible evidence has been found to support the idea that there are at least three different thermal decomposition pathways for CH{sub 3}CHO; namely, radical decomposition: CH{sub 3}CHO +{Delta}{yields} CH{sub 3}+[HCO]{yields} CH{sub 3}+ H + CO; elimination: CH{sub 3}CHO +{Delta}{yields} H{sub 2}+ CH{sub 2}=C=O; isomerization/elimination: CH{sub 3}CHO +{Delta}{yields}[CH{sub 2}=CH-OH]{yields} HC{identical_to}CH + H{sub 2}O. An interesting result is that both PIMS and IR spectroscopy show compelling evidence for the participation of vinylidene, CH{sub 2}=C:, as an intermediate in the decomposition of vinyl alcohol: CH{sub 2}=CH-OH +{Delta}{yields}[CH{sub 2}=C:]+ H{sub 2}O {yields} HC{identical_to}CH + H{sub 2}O.« less

Electrochemical Cobalt-Catalyzed C-H Activation.

PubMed

Sauermann, Nicolas; Meyer, Tjark H; Ackermann, Lutz

2018-06-19

Carbon-heteroatom bonds represent omnipresent structural motifs of the vast majority of functionalized materials and bioactive compounds. C-H activation has emerged as arguably the most efficient strategy to construct C-Het bonds. Despite of major advances, these C-H transformations were largely dominated by precious transition metal catalysts, in combination with stoichiometric, toxic metal oxidants. Herein, we discuss the recent evolution of cobalt-catalyzed C-H activations that enable C-Het formations with electricity as the sole sustainable oxidant until May 2018. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rate Coefficient Measurements of the Reaction CH3 + O2 = CH3O + O

NASA Technical Reports Server (NTRS)

Hwang, S. M.; Ryu, Si-Ok; DeWitt, K. J.; Rabinowitz, M. J.

1999-01-01

Rate coefficients for the reaction CH3 + O2 = CH3O + O were measured behind reflected shock waves in a series of lean CH4-O2-Ar mixtures using hydroxyl and methyl radical diagnostics. The rate coefficients are well represented by an Arrhenius expression given as k = (1.60(sup +0.67, sub -0.47 ) x 10(exp 13) e(-15813 +/- 587 K/T)/cubic cm.mol.s. This expression, which is valid in the temperature range 1575-1822 K, supports the downward trend in the rate coefficients that has been reported in recent determinations. All measurements to date, including the present study, have been to some extent affected by secondary reactions. The complications due to secondary reactions, choice of thermochemical data, and shock-boundary layer interactions that affect the determination of the rate coefficients are examined.

Rate Coefficient Measurements of the Reaction CH3+O2+CH3O+O

NASA Technical Reports Server (NTRS)

Hwang, S. M.; Ryu, Si-Ok; DeWitt, K. J.; Rabinowitz, M. J.

1999-01-01

Rate coefficients for the reaction CH3 + O2 = CH3O + O were measured behind reflected shock waves in a series of lean CH4-O2-Ar mixtures using hydroxyl and methyl radical diagnostics. The rate coefficients are well represented by an Arrhenius expression given as k = (1.60(sup +0.67, -0.47)) X 10(exp 13) exp(- 15813 +/- 587 K/T)cc/mol s. This expression, which is valid in the temperature range 1575-1822 K, supports the downward trend in the rate coefficients that has been reported in recent determinations. All measurements to date, including the present study, have been to some extent affected by secondary reactions. The complications due to secondary reactions, choice of thermochemical data, and shock-boundary layer interactions that affect the determination of the rate coefficients are examined.

pUL34 binding near the human cytomegalovirus origin of lytic replication enhances DNA replication and viral growth.

PubMed

Slayton, Mark; Hossain, Tanvir; Biegalke, Bonita J

2018-05-01

The human cytomegalovirus (HCMV) UL34 gene encodes sequence-specific DNA-binding proteins (pUL34) which are required for viral replication. Interactions of pUL34 with DNA binding sites represses transcription of two viral immune evasion genes, US3 and US9. 12 additional predicted pUL34-binding sites are present in the HCMV genome (strain AD169) with three binding sites concentrated near the HCMV origin of lytic replication (oriLyt). We used ChIP-seq analysis of pUL34-DNA interactions to confirm that pUL34 binds to the oriLyt region during infection. Mutagenesis of the UL34-binding sites in an oriLyt-containing plasmid significantly reduced viral-mediated oriLyt-dependent DNA replication. Mutagenesis of these sites in the HCMV genome reduced the replication efficiencies of the resulting viruses. Protein-protein interaction analyses demonstrated that pUL34 interacts with the viral proteins IE2, UL44, and UL84, that are essential for viral DNA replication, suggesting that pUL34-DNA interactions in the oriLyt region are involved in the DNA replication cascade. Copyright © 2018 Elsevier Inc. All rights reserved.

Tropospheric photooxidation of CF3CH2CHO and CF3(CH2)2CHO initiated by Cl atoms and OH radicals

NASA Astrophysics Data System (ADS)

Antiñolo, M.; Jiménez, E.; Notario, A.; Martínez, E.; Albaladejo, J.

2009-11-01

The absolute rate coefficients for the tropospheric reactions of chlorine (Cl) atoms and hydroxyl (OH) radicals with CF3CH2CHO and CF3(CH2)2CHO were measured as a function of temperature (263-371 K) and pressure (50-215 Torr of He) by pulsed UV laser photolysis techniques. Vacuum UV resonance fluorescence was employed to detect and monitor the time evolution of Cl atoms. Laser induced fluorescence was used in this work as a detection of OH radicals as a function of reaction time. No pressure dependence of the bimolecular rate coefficients, kCl and kOH, was found at all temperatures. At room temperature kCl and kOH were (in 10-11 cm3 molecule-1 s-1): kCl(CF3CH2CHO) = (1.55±0.53); kCl(CF3(CH2)2CHO) = (3.39±1.38); kOH(CF3CH2CHO) = (0.259±0.050); kOH(CF3(CH2)2CHO) = (1.28±0.24). A slightly negative temperature dependence of kCl was observed for CF3CH2CHO and CF3(CH2)2CHO, and kOH(CF3CH2CHO). In contrast, kOH(CF3(CH2)2CHO) did not exhibit a temperature dependence in the studied ranged. Arrhenius expressions for these reactions were: kCl(CF3CH2CHO) =(4.4±1.0) × 10-11 exp{-(316±68)/T} cm3 molecule-1 s-1, kCl(CF3(CH2)2CHO) = (2.9±0.7) × 10-10 exp{-625±80)/T} cm3 molecule-1 s-1, kOH(CF3CH2CHO) = (7.8±2.2) × 10-12 exp{-(314±90)/T} cm3 molecule-1 s-1. The atmospheric impact of the homogeneous removal by OH radicals and Cl atoms of these fluorinated aldehydes is discussed in terms of the global atmospheric lifetimes, taking into account different degradation pathways. The calculated lifetimes show that atmospheric oxidation of CF3(CH2)xCHO are globally dominated by OH radicals, however reactions initiated by Cl atoms can act as a source of free radicals at dawn in the troposphere.

Tropospheric photooxidation of CF3CH2CHO and CF3(CH2)2CHO initiated by Cl atoms and OH radicals

NASA Astrophysics Data System (ADS)

Antiñolo, M.; Jiménez, E.; Notario, A.; Martínez, E.; Albaladejo, J.

2010-02-01

The absolute rate coefficients for the tropospheric reactions of chlorine (Cl) atoms and hydroxyl (OH) radicals with CF3CH2CHO and CF3(CH2)2CHO were measured as a function of temperature (263-371 K) and pressure (50-215 Torr of He) by pulsed UV laser photolysis techniques. Vacuum UV resonance fluorescence was employed to detect and monitor the time evolution of Cl atoms. Laser induced fluorescence was used in this work for the detection of OH radicals as a function of reaction time. No pressure dependence of the bimolecular rate coefficients, kCl and kOH, was found at all temperatures. At room temperature kCl and kOH were (in 10-11 cm3 molecule-1 s-1): kCl(CF3CH2CHO) = (1.55±0.53); kCl(CF3(CH2)2CHO) = (3.39±1.38); kCl(CF3CH2CHO) = (0.259±0.050); kCl(CF3(CH2)2CHO) = (1.28±0.24). A slightly positive temperature dependence of kCl was observed for CF3CH2CHO and CF3(CH2)2CHO, and kOH(CF3CH2CHO). In contrast, kOH(CF3(CH2)2CHO) did not exhibit a temperature dependence over the range investigated. Arrhenius expressions for these reactions were: kCl(CF3CH2CHO) = (4.4±1.0)×10-11 exp{-(316±68)/T} cm3 molecule-1 s-1 kCl(CF3(CH2)2CHO) = (2.9±0.7)×10-10 exp{-(625±80)/T} cm3 molecule-1 s-1 kOH(CF3CH2CHO) = (7.8±2.2)×10-12 exp{-(314±90)/T} cm3 molecule-1 s-1 The atmospheric impact of the homogeneous removal by OH radicals and Cl atoms of these fluorinated aldehydes is discussed in terms of the global atmospheric lifetimes, taking into account different degradation pathways. The calculated lifetimes show that atmospheric oxidation of CF3(CH2)x CHO are globally dominated by OH radicals, however reactions initiated by Cl atoms can act as a source of free radicals at dawn in the troposphere.

Shipboard measurements and modeling of the distribution of CH4 and 13CH4 in the western Pacific

NASA Astrophysics Data System (ADS)

Bromley, T.; Allan, W.; Martin, R.; Mikaloff Fletcher, S. E.; Lowe, D. C.; Struthers, H.; Moss, R.

2012-02-01

We present observations of methane (CH4) mixing ratio and 13C/12C isotopic ratios in CH4 (δ13C) data from a collaborative shipboard project using bulk carrier ships sailing between Nelson, New Zealand, and Osaka, Japan, in the western Pacific Ocean. Measurements of the CH4 mixing ratio and δ13C in CH4were obtained from large clean-air samples collected in each 2.5° to 5° of latitude between 30°S and 30°N on eight voyages from 2004 to 2007. The data show large variations in CH4 mixing ratio in the tropical western Pacific, and data analysis suggests that these large variations are related to the positions and strengths of the South Pacific Convergence Zone and the Intertropical Convergence Zone, with variability in the sources playing a much smaller role. These measurements are compared with results from a modified version of the Unified Model (UMeth) general circulation model along two transects, one similar to the ship transects and another 18.75° to the east. Although UMeth was run to a steady state with the same sources and sinks each year, the gradient structures varied considerably from year to year, supporting our conclusion that variability in transport is a major driver for the observed variations in CH4. Simulations forced with an idealized representation of the El Niño-Southern Oscillation (ENSO) suggest that a large component of the observed variability in latitudinal gradients of CH4 and its δ13C arises from intrinsic variability in the climate system that does not occur on ENSO time scales.

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data.

PubMed

Ambrosini, Giovanna; Dreos, René; Kumar, Sunil; Bucher, Philipp

2016-11-18

ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data. Here we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware. The web interface provides access to a large database of public data. The ChIP-Seq tools have a modular and interoperable design in that the output from one application can serve as input to another one. Complex and innovative tasks can thus be achieved by running several tools in a cascade. The various ChIP-Seq command line tools and web services either complement or compare favorably to related bioinformatics resources in terms of computational efficiency, ease of access to public data and interoperability with other web-based tools. The ChIP-Seq server is accessible at http://ccg.vital-it.ch/chipseq/ .

Anomalous torsional tripling in the ν9 and ν10 CH3-deformation modes of ethane 12CH313CH3

NASA Astrophysics Data System (ADS)

Lattanzi, F.; di Lauro, C.

2017-12-01

We have investigated the anomalous torsional behavior in the coupled ν9 and ν10 vibrational fundamentals of 12CH313CH3, both states exhibiting a splitting into three components, instead of two, only in those rotational levels which are very close to resonance. We conclude that the intrinsic additional splitting, which occurs in the E-torsional components, for these two vibrational states is too small to be detected in the high resolution infrared spectrum, but it is substantively enhanced by their coupling. It is shown that this effect requires the simultaneous action of torsion independent operators, such as Fermi-type and z-Coriolis, not allowed in the more symmetric isotopologue 12CH312CH3, and torsion dependent operators, such as torsional-Coriolis, connecting the two vibrational states. Our conclusions lead to a simple model for the coupling of ν9 and ν10, with effective Fermi-type matrix elements W for the A-torsional components, and W ± w for the two pairs of E-torsional components. This causes the additional splitting in the E-pairs. This model is consistent with the mechanism causing the Coriolis-dependent decrease of the A-E torsional splitting in degenerate vibrational states. Exploratory calculations were performed making use of results from a normal mode analysis, showing that the effects predictable by the proposed model are of the correct order of magnitude compared to the observed features, with coupling parameter values reasonably consistent with those determined by the least squares fit of the observed transition wavenumbers.

Isotopic signatures of anthropogenic CH4 sources in Alberta, Canada

NASA Astrophysics Data System (ADS)

Lopez, M.; Sherwood, O. A.; Dlugokencky, E. J.; Kessler, R.; Giroux, L.; Worthy, D. E. J.

2017-09-01

A mobile system was used for continuous ambient measurements of stable CH4 isotopes (12CH4 and 13CH4) and ethane (C2H6). This system was used during a winter mobile campaign to investigate the CH4 isotopic signatures and the C2H6/CH4 ratios of the main anthropogenic sources of CH4 in the Canadian province of Alberta. Individual signatures were derived from δ13CH4 and C2H6 measurements in plumes arriving from identifiable single sources. Methane emissions from beef cattle feedlots (n = 2) and landfill (n = 1) had δ13CH4 signatures of -66.7 ± 2.4‰ and -55.3 ± 0.2‰, respectively. The CH4 emissions associated with the oil or gas industry had distinct δ13CH4 signatures, depending on the formation process. Emissions from oil storage tanks (n = 5) had δ13CH4 signatures ranging from -54.9 ± 2.9‰ to -60.6 ± 0.6‰ and non-detectable C2H6, characteristic of secondary microbial methanogenesis in oil-bearing reservoirs. In contrast, CH4 emissions associated with natural gas facilities (n = 8) had δ13CH4 signatures ranging from -41.7 ± 0.7‰ to -49.7 ± 0.7‰ and C2H6/CH4 molar ratios of 0.10 for raw natural gas to 0.04 for processed/refined natural gas, consistent with thermogenic origins. These isotopic signatures and C2H6/CH4 ratios have been used for source discrimination in the weekly atmospheric measurements of stable CH4 isotopes over a two-month winter period at the Lac La Biche (LLB) measurement station, located in Alberta, approximately 200 km northeast of Edmonton. The average signature of -59.5 ± 1.4‰ observed at LLB is likely associated with transport of air after passing over oil industry sources located south of the station.

Cloning of the Alcaligenes latus polyhydroxyalkanoate biosynthesis genes and use of these genes for enhanced production of Poly(3-hydroxybutyrate) in Escherichia coli.

PubMed

Choi, J I; Lee, S Y; Han, K

1998-12-01

Polyhydroxyalkanoates (PHAs) are microbial polyesters that can be used as completely biodegradable polymers, but the high production cost prevents their use in a wide range of applications. Recombinant Escherichia coli strains harboring the Ralstonia eutropha PHA biosynthesis genes have been reported to have several advantages as PHA producers compared with wild-type PHA-producing bacteria. However, the PHA productivity (amount of PHA produced per unit volume per unit time) obtained with these recombinant E. coli strains has been lower than that obtained with the wild-type bacterium Alcaligenes latus. To endow the potentially superior PHA biosynthetic machinery to E. coli, we cloned the PHA biosynthesis genes from A. latus. The three PHA biosynthesis genes formed an operon with the order PHA synthase, beta-ketothiolase, and reductase genes and were constitutively expressed from the natural promoter in E. coli. Recombinant E. coli strains harboring the A. latus PHA biosynthesis genes accumulated poly(3-hydroxybutyrate) (PHB), a model PHA product, more efficiently than those harboring the R. eutropha genes. With a pH-stat fed-batch culture of recombinant E. coli harboring a stable plasmid containing the A. latus PHA biosynthesis genes, final cell and PHB concentrations of 194.1 and 141.6 g/liter, respectively, were obtained, resulting in a high productivity of 4.63 g of PHB/liter/h. This improvement should allow recombinant E. coli to be used for the production of PHB with a high level of economic competitiveness.

ChAT-ChR2-EYFP mice have enhanced motor endurance but show deficits in attention and several additional cognitive domains.

PubMed

Kolisnyk, Benjamin; Guzman, Monica S; Raulic, Sanda; Fan, Jue; Magalhães, Ana C; Feng, Guoping; Gros, Robert; Prado, Vania F; Prado, Marco A M

2013-06-19

Acetylcholine (ACh) is an important neuromodulator in the nervous system implicated in many forms of cognitive and motor processing. Recent studies have used bacterial artificial chromosome (BAC) transgenic mice expressing channelrhodopsin-2 (ChR2) protein under the control of the choline acetyltransferase (ChAT) promoter (ChAT-ChR2-EYFP) to dissect cholinergic circuit connectivity and function using optogenetic approaches. We report that a mouse line used for this purpose also carries several copies of the vesicular acetylcholine transporter gene (VAChT), which leads to overexpression of functional VAChT and consequently increased cholinergic tone. We demonstrate that these mice have marked improvement in motor endurance. However, they also present severe cognitive deficits, including attention deficits and dysfunction in working memory and spatial memory. These results suggest that increased VAChT expression may disrupt critical steps in information processing. Our studies demonstrate that ChAT-ChR2-EYFP mice show altered cholinergic tone that fundamentally differentiates them from wild-type mice.

CH4 production via CO2 reduction in a temperate bog - A source of (C-13)-depleted CH4

NASA Technical Reports Server (NTRS)

Lansdown, J. M.; Quay, P. D.; King, S. L.

1992-01-01

The paper reports measurements, taken over two annual cycles, of the flux and delta(C-13) of CH4 released from an acidic peat bog located in the foothills of the Cascade Range in Washington state, U.S. Measurements of the rate of aceticlastic methanogenesis and CO2 reduction in peat soil, using (C-14)-labeled acetate and sodium bicarbonate, show that acetate was not an important CH4 precursor and that CO2 reduction could account for all of the CH4 production. The in situ kinetic isotope effect for CO2 reduction, calculated using the delta-(C-13) of soil water CO2 and CH4 flux, was 0.932 +/- 0.007.

ChLae1 and ChVel1 Regulate T-toxin Production, Virulence, Oxidative Stress Response, and Development of the Maize Pathogen Cochliobolus heterostrophus

PubMed Central

Wu, Dongliang; Oide, Shinichi; Zhang, Ning; Choi, May Yee; Turgeon, B. Gillian

2012-01-01

LaeA and VeA coordinate secondary metabolism and differentiation in response to light signals in Aspergillus spp. Their orthologs, ChLae1 and ChVel1, were identified in the maize pathogen Cochliobolus heterostrophus, known to produce a wealth of secondary metabolites, including the host selective toxin, T-toxin. Produced by race T, T-toxin promotes high virulence to maize carrying Texas male sterile cytoplasm (T-cms). T-toxin production is significantly increased in the dark in wild type (WT), whereas Chvel1 and Chlae1 mutant toxin levels are much reduced in the dark compared to WT. Correspondingly, expression of T-toxin biosynthetic genes (Tox1) is up-regulated in the dark in WT, while dark-induced expression is much reduced/minimal in Chvel1 and Chlae1 mutants. Toxin production and Tox1 gene expression are increased in ChVEL1 overexpression (OE) strains grown in the dark and in ChLAE1 strains grown in either light or dark, compared to WT. These observations establish ChLae1 and ChVel1 as the first factors known to regulate host selective toxin production. Virulence of Chlae1 and Chvel1 mutants and OE strains is altered on both T-cms and normal cytoplasm maize, indicating that both T-toxin mediated super virulence and basic pathogenic ability are affected. Deletion of ChLAE1 or ChVEL1 reduces tolerance to H2O2. Expression of CAT3, one of the three catalase genes, is reduced in the Chvel1 mutant. Chlae1 and Chvel1 mutants also show decreased aerial hyphal growth, increased asexual sporulation and female sterility. ChLAE1 OE strains are female sterile, while ChVEL1 OE strains are more fertile than WT. ChLae1 and ChVel1 repress expression of 1,8-dihydroxynaphthalene (DHN) melanin biosynthesis genes, and, accordingly, melanization is enhanced in Chlae1 and Chvel1 mutants, and reduced in OE strains. Thus, ChLae1 and ChVel1 positively regulate T-toxin biosynthesis, pathogenicity and super virulence, oxidative stress responses, sexual development, and aerial hyphal

CO2 CH4 and N20 fluxes during land conversion in early bioenergy systems

NASA Astrophysics Data System (ADS)

Zenone, T.

2012-04-01

CO2 CH4 and N20 fluxes during land conversion in early bioenergy systems Terenzio Zenone1-2, Jiquan Chen1-2, Ilya Gelfand3-4, G. Philip Robertson3-4 1 Department of Environmental Sciences, University of Toledo, Toledo, OH USA 2 Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI USA 3 W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI USA 4Department of Crop and Soil Sciences, Michigan State University, East Lansing, MI USA Environmental sustainability of bioenergy crop cultivation represents an important challenge and is a topic of intensive scientific and political debate worldwide due to increasing societal needs for renewable energy. Despite the increasing knowledge related to potential bioenergy systems, the effect of land use change (LUC) on GHG fluxes during the conversion remains poorly understood but is likely to be substantial. In order to tackle this issue the Great lake Bioenergy Research Center (GLBRC) of the US Department of Energy (DOE) has established a field experiment and deployed a cluster of eddy-covariance towers to quantify the magnitude and changes of ecosystem carbon assimilation, loss, and balance during the conversion and establishment years in a permanent prairie and four types of candidate biofuel systems [Conservation Reserve Program (CRP) grassland, switchgrass, mixed-species restored prairie and corn]. Six sites were converted to soybean in 2009 before establishing the bioenergy systems in 2010 while one site was kept grassland as reference. Soil N2O and CH4 fluxes were measured biweekly with static chambers in four replicate locations in each fields, within the footprint of the eddy covariance tower using static chamber GHG flux protocols of the KBS LTER site. Our field observations, made between January 2009 through December 2010, showed that conversion of CRP to soybean induced net C emissions during the conversion year that ranging from 288 g C m-2, to 173 g C m-2 . while

Infrared absorption of 1-chloro-2-methyl-2-propyl [⋅C(CH3)2CH2Cl] and 2-chloro-2-methylpropyl [⋅CH2C(CH3)2Cl] radicals produced in the addition reactions of Cl with isobutene (i-C4H8) in solid para-hydrogen.

PubMed

Chou, Ching-Yin; Lee, Yuan-Pern

2016-10-07

The addition reactions of chlorine atom with isobutene (i-C 4 H 8 ) in solid para-hydrogen (p-H 2 ) were investigated with infrared (IR) absorption spectra. When a p-H 2 matrix containing Cl 2 and isobutene was irradiated with ultraviolet light at 365 nm, intense lines in a set at 534.5, 1001.0, 1212.9, 1366.0, 2961.6, and 2934.7 cm -1 , and several weaker others due to the 1-chloro-2-methyl-2-propyl radical, ⋅ C(CH 3 ) 2 CH 2 Cl, and those in a second set including intense ones at 642.7, 799.2, 1098.2, 1371.8, and 3027.3 cm -1 due to the 2-chloro-2-methylpropyl radical, ⋅ CH 2 C(CH 3 ) 2 Cl, appeared; the ratio of ⋅ C(CH 3 ) 2 CH 2 Cl to ⋅ CH 2 C(CH 3 ) 2 Cl was approximately (3 ± 1):1. The observed wavenumbers and relative intensities agree with the vibrational wavenumbers and IR intensities predicted with the B3PW91/aug-cc-pVTZ method. That the Cl atom adds to both carbons of the C=C bond of isobutene with the terminal site slightly favored is consistent with the energies of products predicted theoretically, but is in contrast to the reaction of Cl + propene in solid p-H 2 in which the addition of Cl to mainly the central C atom was previously reported. The role of the p-H 2 matrix in affecting the reaction paths is discussed. Absorption lines of the complex i-C 4 H 8 ⋅Cl 2 and the dichloro-product anti-1,2-dichloro-2-methylpropane, a-CH 2 ClCCl(CH 3 ) 2 , are also characterized.

Landscape patterns of CH4 fluxes in an alpine tundra ecosystem

USGS Publications Warehouse

West, A.E.; Brooks, P.D.; Fisk, M.C.; Smith, Lesley K.; Holland, E.A.; Jaeger, C. H.; Babcock, S.; Lai, R.S.; Schmidt, S.K.

1999-01-01

We measured CH4 fluxes from three major plant communities characteristic of alpine tundra in the Colorado Front Range. Plant communities in this ecosystem are determined by soil moisture regimes induced by winter snowpack distribution. Spatial patterns of CH4 flux during the snow-free season corresponded roughly with these plant communities. In Carex-dominated meadows, which receive the most moisture from snowmelt, net CH4 production occurred. However, CH4 production in one Carex site (seasonal mean = +8.45 mg CH4 m-2 d-1) was significantly larger than in the other Carex sites (seasonal means = -0.06 and +0.05 mg CH4 m-2 d-1). This high CH4 flux may have resulted from shallower snowpack during the winter. In Acomastylis meadows, which have an intermediate moisture regime, CH4 oxidation dominated (seasonal mean = -0.43 mg CH4 m-2 d-1). In the windswept Kobresia meadow plant community, which receive the least amount of moisture from snowmelt, only CH4 oxidation was observed (seasonal mean = -0.77 mg CH4 m-2 d-1). Methane fluxes correlated with a different set of environmental factors within each plant community. In the Carex plant community, CH4 emission was limited by soil temperature. In the Acomastylis meadows, CH4 oxidation rates correlated positively with soil temperature and negatively with soil moisture. In the Kobresia community, CH4 oxidation was stimulated by precipitation. Thus, both snow-free season CH4 fluxes and the controls on those CH4 fluxes were related to the plant communities determined by winter snowpack.

Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq.

PubMed

Guertin, Michael J; Cullen, Amy E; Markowetz, Florian; Holding, Andrew N

2018-04-17

A key challenge in quantitative ChIP combined with high-throughput sequencing (ChIP-seq) is the normalization of data in the presence of genome-wide changes in occupancy. Analysis-based normalization methods were developed for transcriptomic data and these are dependent on the underlying assumption that total transcription does not change between conditions. For genome-wide changes in transcription factor (TF) binding, these assumptions do not hold true. The challenges in normalization are confounded by experimental variability during sample preparation, processing and recovery. We present a novel normalization strategy utilizing an internal standard of unchanged peaks for reference. Our method can be readily applied to monitor genome-wide changes by ChIP-seq that are otherwise lost or misrepresented through analytical normalization. We compare our approach to normalization by total read depth and two alternative methods that utilize external experimental controls to study TF binding. We successfully resolve the key challenges in quantitative ChIP-seq analysis and demonstrate its application by monitoring the loss of Estrogen Receptor-alpha (ER) binding upon fulvestrant treatment, ER binding in response to estrodiol, ER mediated change in H4K12 acetylation and profiling ER binding in patient-derived xenographs. This is supported by an adaptable pipeline to normalize and quantify differential TF binding genome-wide and generate metrics for differential binding at individual sites.

ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries.

PubMed

Nair, Nishanth Ulhas; Sahu, Avinash Das; Bucher, Philipp; Moret, Bernard M E

2012-01-01

The advent of high-throughput technologies such as ChIP-seq has made possible the study of histone modifications. A problem of particular interest is the identification of regions of the genome where different cell types from the same organism exhibit different patterns of histone enrichment. This problem turns out to be surprisingly difficult, even in simple pairwise comparisons, because of the significant level of noise in ChIP-seq data. In this paper we propose a two-stage statistical method, called ChIPnorm, to normalize ChIP-seq data, and to find differential regions in the genome, given two libraries of histone modifications of different cell types. We show that the ChIPnorm method removes most of the noise and bias in the data and outperforms other normalization methods. We correlate the histone marks with gene expression data and confirm that histone modifications H3K27me3 and H3K4me3 act as respectively a repressor and an activator of genes. Compared to what was previously reported in the literature, we find that a substantially higher fraction of bivalent marks in ES cells for H3K27me3 and H3K4me3 move into a K27-only state. We find that most of the promoter regions in protein-coding genes have differential histone-modification sites. The software for this work can be downloaded from http://lcbb.epfl.ch/software.html.

On the Formation of the C2H6O Isomers Ethanol (C2H5OH) and Dimethyl Ether (CH3OCH3) in Star-forming Regions

NASA Astrophysics Data System (ADS)

Bergantini, Alexandre; Maksyutenko, Pavlo; Kaiser, Ralf I.

2017-06-01

The structural isomers ethanol (CH3CH2OH) and dimethyl ether (CH3OCH3) were detected in several low-, intermediate-, and high-mass star-forming regions, including Sgr B2, Orion, and W33A, with the relative abundance ratios of ethanol/dimethyl ether varying from about 0.03 to 3.4. Until now, no experimental data regarding the formation mechanisms and branching ratios of these two species in laboratory simulation experiments could be provided. Here, we exploit tunable photoionization reflectron time-of-flight mass spectrometry (PI-ReTOF-MS) to detect and analyze the production of complex organic molecules (COMs) resulting from the exposure of water/methane (H2O/CH4) ices to energetic electrons. The main goal is to understand the formation mechanisms in star-forming regions of two C2H6O isomers: ethanol (CH3CH2OH) and dimethyl ether (CH3OCH3). The results show that the experimental branching ratios favor the synthesis of ethanol versus dimethyl ether (31 ± 11:1). This finding diverges from the abundances observed toward most star-forming regions, suggesting that production routes on interstellar grains to form dimethyl ether might be missing; alternatively, ethanol can be overproduced in the present simulation experiments, such as via radical-radical recombination pathways involving ethyl and hydroxyl radicals. Finally, the PI-ReTOF-MS data suggest the formation of methylacetylene (C3H4), ketene (CH2CO), propene (C3H6), vinyl alcohol (CH2CHOH), acetaldehyde (CH3CHO), and methyl hydroperoxide (CH3OOH), in addition to ethane (C2H6), methanol (CH3OH), and CO2 detected from infrared spectroscopy. The yield of all the confirmed species is also determined.

Room-temperature enantioselective C-H iodination via kinetic resolution.

PubMed

Chu, Ling; Xiao, Kai-Jiong; Yu, Jin-Quan

2014-10-24

Asymmetric carbon-hydrogen (C-H) activation reactions often rely on desymmetrization of prochiral C-H bonds on the same achiral molecule, using a chiral catalyst. Here, we report a kinetic resolution via palladium-catalyzed enantioselective C-H iodination in which one of the enantiomers of a racemic benzylic amine substrates undergoes faster aryl C-H insertion with the chiral catalysts than the other. The resulting enantioenriched C-H functionalization products would not be accessible through desymmetrization of prochiral C-H bonds. The exceedingly high relative rate ratio (k(fast)/k(slow) up to 244), coupled with the subsequent iodination of the remaining enantiomerically enriched starting material using a chiral ligand with the opposite configuration, enables conversion of both substrate enantiomers into enantiomerically pure iodinated products. Copyright © 2014, American Association for the Advancement of Science.

Direct dynamics simulation of dioxetane formation and decomposition via the singlet .O-O-CH2-CH2. biradical: Non-RRKM dynamics

NASA Astrophysics Data System (ADS)

Sun, Rui; Park, Kyoyeon; de Jong, Wibe A.; Lischka, Hans; Windus, Theresa L.; Hase, William L.

2012-07-01

Electronic structure calculations and direct chemical dynamics simulations are used to study the formation and decomposition of dioxetane on its ground state singlet potential energy surface. The stationary points for 1O2 + C2H4, the singlet .O-O-CH2-CH2. biradical, the transition state (TS) connecting this biradical with dioxetane, and the two transition states and gauche .O-CH2-CH2-O. biradical connecting dioxetane with the formaldehyde product molecules are investigated at different levels of electronic structure theory including UB3LYP, UMP2, MRMP2, and CASSCF and a range of basis sets. The UB3LYP/6-31G* method was found to give representative energies for the reactive system and was used as a model for the simulations. UB3LYP/6-31G* direct dynamics trajectories were initiated at the TS connecting the .O-O-CH2-CH2. biradical and dioxetane by sampling the TS's vibrational energy levels, and rotational and reaction coordinate energies, with Boltzmann distributions at 300, 1000, and 1500 K. This corresponds to the transition state theory model for trajectories that pass the TS. The trajectories were directed randomly towards both the biradical and dioxetane. A small fraction of the trajectories directed towards the biradical recrossed the TS and formed dioxetane. The remainder formed 1O2 + C2H4 and of these ˜ 40% went directly from the TS to 1O2 + C2H4 without getting trapped and forming an intermediate in the .O-O-CH2-CH2. biradical potential energy minimum, a non-statistical result. The dioxetane molecules which are formed dissociate to two formaldehyde molecules with a rate constant two orders of magnitude smaller than that predicted by Rice-Ramsperger-Kassel-Marcus theory. The reaction dynamics from dioxetane to the formaldehyde molecules do not follow the intrinsic reaction coordinate or involve trapping in the gauche .O-CH2-CH2-O. biradical potential energy minimum. Important non-statistical dynamics are exhibited for this reactive system.

C-H bond activation of hydrocarbons by an imidozirconocene complex.

PubMed

Hoyt, Helen M; Michael, Forrest E; Bergman, Robert G

2004-02-04

Monomeric imidozirconocene complexes of the type Cp2(L)Zr=NCMe3 (Cp = cyclopentadienyl, L = Lewis base) have been shown to activate the carbon-hydrogen bonds of benzene, but not the C-H bonds of saturated hydrocarbons. To our knowledge, this singularly important class of C-H activation reactions has heretofore not been observed in imidometallocene systems. The M=NR bond formed on heating the racemic ethylenebis(tetrahydro)indenyl methyl tert-butyl amide complex, however, cleanly and quantitatively activates a wide range of n-alkane, alkene, and arene C-H bonds. Mechanistic experiments support the proposal of intramolecular elimination of methane followed by a concerted addition of the hydrocarbon C-H bond. Products formed by activation of sp2 C-H bonds are generally more thermodynamically stable than those formed by activation of sp3 C-H bonds, and those resulting from reaction at primary C-H bonds are preferred over secondary sp3 C-H activation products. There is also evidence that thermodynamic selectivity among C-H bonds is sterically rather than electronically controlled.

Mapping pan-Arctic CH4 emissions using an adjoint method by integrating process-based wetland and lake biogeochemical models and atmospheric CH4 concentrations

NASA Astrophysics Data System (ADS)

Tan, Z.; Zhuang, Q.; Henze, D. K.; Frankenberg, C.; Dlugokencky, E. J.; Sweeney, C.; Turner, A. J.

2015-12-01

Understanding CH4 emissions from wetlands and lakes are critical for the estimation of Arctic carbon balance under fast warming climatic conditions. To date, our knowledge about these two CH4 sources is almost solely built on the upscaling of discontinuous measurements in limited areas to the whole region. Many studies indicated that, the controls of CH4 emissions from wetlands and lakes including soil moisture, lake morphology and substrate content and quality are notoriously heterogeneous, thus the accuracy of those simple estimates could be questionable. Here we apply a high spatial resolution atmospheric inverse model (nested-grid GEOS-Chem Adjoint) over the Arctic by integrating SCIAMACHY and NOAA/ESRL CH4 measurements to constrain the CH4 emissions estimated with process-based wetland and lake biogeochemical models. Our modeling experiments using different wetland CH4 emission schemes and satellite and surface measurements show that the total amount of CH4 emitted from the Arctic wetlands is well constrained, but the spatial distribution of CH4 emissions is sensitive to priors. For CH4 emissions from lakes, our high-resolution inversion shows that the models overestimate CH4 emissions in Alaskan costal lowlands and East Siberian lowlands. Our study also indicates that the precision and coverage of measurements need to be improved to achieve more accurate high-resolution estimates.

Soil-atmospheric exchange of CO2, CH4, and N2O in three subtropical forest ecosystems in southern China

USGS Publications Warehouse

Tang, X.; Liu, S.; Zhou, G.; Zhang, Dongxiao; Zhou, C.

2006-01-01

The magnitude, temporal, and spatial patterns of soil-atmospheric greenhouse gas (hereafter referred to as GHG) exchanges in forests near the Tropic of Cancer are still highly uncertain. To contribute towards an improvement of actual estimates, soil-atmospheric CO2, CH4, and N2O fluxes were measured in three successional subtropical forests at the Dinghushan Nature Reserve (hereafter referred to as DNR) in southern China. Soils in DNR forests behaved as N2O sources and CH4 sinks. Annual mean CO2, N2O, and CH4 fluxes (mean ?? SD) were 7.7 ?? 4.6MgCO2-Cha-1 yr-1, 3.2 ?? 1.2 kg N2ONha-1 yr-1, and 3.4 ?? 0.9 kgCH4-Cha-1 yr-1, respectively. The climate was warm and wet from April through September 2003 (the hot-humid season) and became cool and dry from October 2003 through March 2004 (the cool-dry season). The seasonality of soil CO2 emission coincided with the seasonal climate pattern, with high CO2 emission rates in the hot-humid season and low rates in the cool-dry season. In contrast, seasonal patterns of CH4 and N2O fluxes were not clear, although higher CH4 uptake rates were often observed in the cool-dry season and higher N2O emission rates were often observed in the hot-humid season. GHG fluxes measured at these three sites showed a clear increasing trend with the progressive succession. If this trend is representative at the regional scale, CO2 and N2O emissions and CH4 uptake in southern China may increase in the future in light of the projected change in forest age structure. Removal of surface litter reduced soil CO2 effluxes by 17-44% in the three forests but had no significant effect on CH4 absorption and N2O emission rates. This suggests that microbial CH4 uptake and N2O production was mainly related to the mineral soil rather than in the surface litter layer. ?? 2006 Blackwell Publishing Ltd.

Frequency and Pathological Phenotype of Bovine Astrovirus CH13/NeuroS1 Infection in Neurologically-Diseased Cattle: Towards Assessment of Causality.

PubMed

Selimovic-Hamza, Senija; Boujon, Céline L; Hilbe, Monika; Oevermann, Anna; Seuberlich, Torsten

2017-01-18

Next-generation sequencing (NGS) has opened up the possibility of detecting new viruses in unresolved diseases. Recently, astrovirus brain infections have been identified in neurologically diseased humans and animals by NGS, among them bovine astrovirus (BoAstV) CH13/NeuroS1, which has been found in brain tissues of cattle with non-suppurative encephalitis. Only a few studies are available on neurotropic astroviruses and a causal relationship between BoAstV CH13/NeuroS1 infections and neurological disease has been postulated, but remains unproven. Aiming at making a step forward towards assessing the causality, we collected brain samples of 97 cases of cattle diagnosed with unresolved non-suppurative encephalitis, and analyzed them by in situ hybridization and immunohistochemistry, to determine the frequency and neuropathological distribution of the BoAstV CH13/NeuroS1 and its topographical correlation to the pathology. We detected BoAstV CH13/NeuroS1 RNA or proteins in neurons throughout all parts of the central nervous system (CNS) in 34% of all cases, but none were detected in cattle of the control group. In general, brain lesions had a high correlation with the presence of the virus. These findings show that a substantial proportion of cattle with non-suppurative encephalitis are infected with BoAstV CH13/NeuroS1 and further substantiate the causal relationship between neurological disease and astrovirus infections.

Frequency and Pathological Phenotype of Bovine Astrovirus CH13/NeuroS1 Infection in Neurologically-Diseased Cattle: Towards Assessment of Causality

PubMed Central

Selimovic-Hamza, Senija; Boujon, Céline L.; Hilbe, Monika; Oevermann, Anna; Seuberlich, Torsten

2017-01-01

Next-generation sequencing (NGS) has opened up the possibility of detecting new viruses in unresolved diseases. Recently, astrovirus brain infections have been identified in neurologically diseased humans and animals by NGS, among them bovine astrovirus (BoAstV) CH13/NeuroS1, which has been found in brain tissues of cattle with non-suppurative encephalitis. Only a few studies are available on neurotropic astroviruses and a causal relationship between BoAstV CH13/NeuroS1 infections and neurological disease has been postulated, but remains unproven. Aiming at making a step forward towards assessing the causality, we collected brain samples of 97 cases of cattle diagnosed with unresolved non-suppurative encephalitis, and analyzed them by in situ hybridization and immunohistochemistry, to determine the frequency and neuropathological distribution of the BoAstV CH13/NeuroS1 and its topographical correlation to the pathology. We detected BoAstV CH13/NeuroS1 RNA or proteins in neurons throughout all parts of the central nervous system (CNS) in 34% of all cases, but none were detected in cattle of the control group. In general, brain lesions had a high correlation with the presence of the virus. These findings show that a substantial proportion of cattle with non-suppurative encephalitis are infected with BoAstV CH13/NeuroS1 and further substantiate the causal relationship between neurological disease and astrovirus infections. PMID:28106800

Thermodynamic and hydrochemical controls on CH4 in a coal seam gas and overlying alluvial aquifer: new insights into CH4 origins

PubMed Central

Owen, D. Des. R.; Shouakar-Stash, O.; Morgenstern, U.; Aravena, R.

2016-01-01

Using a comprehensive data set (dissolved CH4, δ13C-CH4, δ2H-CH4, δ13C-DIC, δ37Cl, δ2H-H2O, δ18O-H2O, Na, K, Ca, Mg, HCO3, Cl, Br, SO4, NO3 and DO), in combination with a novel application of isometric log ratios, this study describes hydrochemical and thermodynamic controls on dissolved CH4 from a coal seam gas reservoir and an alluvial aquifer in the Condamine catchment, eastern Surat/north-western Clarence-Moreton basins, Australia. δ13C-CH4 data in the gas reservoir (−58‰ to −49‰) and shallow coal measures underlying the alluvium (−80‰ to −65‰) are distinct. CO2 reduction is the dominant methanogenic pathway in all aquifers, and it is controlled by SO4 concentrations and competition for reactants such as H2. At isolated, brackish sites in the shallow coal measures and alluvium, highly depleted δ2H-CH4 (<310‰) indicate acetoclastic methanogenesis where SO4 concentrations inhibit CO2 reduction. Evidence of CH4 migration from the deep gas reservoir (200–500 m) to the shallow coal measures (<200 m) or the alluvium was not observed. The study demonstrates the importance of understanding CH4 at different depth profiles within and between aquifers. Further research, including culturing studies of microbial consortia, will improve our understanding of the occurrence of CH4 within and between aquifers in these basins. PMID:27578542

A vacuum ultraviolet laser pulsed field ionization-photoion study of methane (CH 4): Determination of the appearance energy of methylium from methane with unprecedented precision and the resulting impact on the bond dissociation energies of CH 4 and CH 4 +

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

Chang, Yih -Chung; Xiong, Bo; Bross, David H.

Here, we report on the successful implementation of a high-resolution vacuum ultraviolet (VUV) laser pulsed field ionization-photoion (PFI-PI) detection method for the study of unimolecular dissociation of quantum-state- or energy-selected molecular ions. As a test case, we have determined the 0 K appearance energy (AE 0) for the formation of methylium, CH 3 +, from methane, CH 4, as AE 0 (CH 3 +/CH 4) = 14.32271 ± 0.00013 eV. This value has a significantly smaller error limit, but is otherwise consistent with previous laboratory and/or synchrotron-based studies of this dissociative photoionization onset. Furthermore, the sum of the VUV lasermore » PFI-PI spectra obtained for the parent CH 4 + ion and the fragment CH 3 + ions of methane is found to agree with the earlier VUV pulsed field ionization-photoelectron (VUV-PFI-PE) spectrum of methane, providing unambiguous validation of the previous interpretation that the sharp VUV-PFI-PE step observed at the AE 0 (CH 3 +/CH 4) threshold ensues because of higher PFI detection efficiency for fragment CH 3 + than for parent CH 4 +. This, in turn, is a consequence of the underlying high- n Rydberg dissociation mechanism for the dissociative photoionization of CH 4, which was proposed in previous synchrotron-based VUV-PFI-PE and VUV-PFI-PEPICO studies of CH 4. The present highly accurate 0 K dissociative ionization threshold for CH 4 can be utilized to derive accurate values for the bond dissociation energies of methane and methane cation. For methane, the straightforward application of sequential thermochemistry via the positive ion cycle leads to some ambiguity because of two competing VUV-PFI-PE literature values for the ionization energy of methyl radical. The ambiguity is successfully resolved by applying the Active Thermochemical Tables (ATcT) approach, resulting in D 0 (H-CH 3) = 432.463 ± 0.027 kJ/mol and D 0(H-CH 3 +) = 164.701 ± 0.038 kJ/mol.« less

A vacuum ultraviolet laser pulsed field ionization-photoion study of methane (CH 4): Determination of the appearance energy of methylium from methane with unprecedented precision and the resulting impact on the bond dissociation energies of CH 4 and CH 4 +

DOE PAGES

Chang, Yih -Chung; Xiong, Bo; Bross, David H.; ...

2017-03-27

Here, we report on the successful implementation of a high-resolution vacuum ultraviolet (VUV) laser pulsed field ionization-photoion (PFI-PI) detection method for the study of unimolecular dissociation of quantum-state- or energy-selected molecular ions. As a test case, we have determined the 0 K appearance energy (AE 0) for the formation of methylium, CH 3 +, from methane, CH 4, as AE 0 (CH 3 +/CH 4) = 14.32271 ± 0.00013 eV. This value has a significantly smaller error limit, but is otherwise consistent with previous laboratory and/or synchrotron-based studies of this dissociative photoionization onset. Furthermore, the sum of the VUV lasermore » PFI-PI spectra obtained for the parent CH 4 + ion and the fragment CH 3 + ions of methane is found to agree with the earlier VUV pulsed field ionization-photoelectron (VUV-PFI-PE) spectrum of methane, providing unambiguous validation of the previous interpretation that the sharp VUV-PFI-PE step observed at the AE 0 (CH 3 +/CH 4) threshold ensues because of higher PFI detection efficiency for fragment CH 3 + than for parent CH 4 +. This, in turn, is a consequence of the underlying high- n Rydberg dissociation mechanism for the dissociative photoionization of CH 4, which was proposed in previous synchrotron-based VUV-PFI-PE and VUV-PFI-PEPICO studies of CH 4. The present highly accurate 0 K dissociative ionization threshold for CH 4 can be utilized to derive accurate values for the bond dissociation energies of methane and methane cation. For methane, the straightforward application of sequential thermochemistry via the positive ion cycle leads to some ambiguity because of two competing VUV-PFI-PE literature values for the ionization energy of methyl radical. The ambiguity is successfully resolved by applying the Active Thermochemical Tables (ATcT) approach, resulting in D 0 (H-CH 3) = 432.463 ± 0.027 kJ/mol and D 0(H-CH 3 +) = 164.701 ± 0.038 kJ/mol.« less

FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes.

PubMed

Parodi, Alice C L; Sangalli, Laura M; Vantini, Simone; Amati, Bruno; Secchi, Piercesare; Morelli, Marco J

2017-08-15

Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) generates local accumulations of sequencing reads on the genome ("peaks"), which correspond to specific protein-DNA interactions or chromatin modifications. Peaks are detected by considering their total area above a background signal, usually neglecting their shapes, which instead may convey additional biological information. We present FunChIP, an R/Bioconductor package for clustering peaks according to a functional representation of their shapes: after approximating their profiles with cubic B-splines, FunChIP minimizes their functional distance and classifies the peaks applying a k-mean alignment and clustering algorithm. The whole pipeline is user-friendly and provides visualization functions for a quick inspection of the results. An application to the transcription factor Myc in 3T9 murine fibroblasts shows that clusters of peaks with different shapes are associated with different genomic locations and different transcriptional regulatory activity. The package is implemented in R and is available under Artistic Licence 2.0 from the Bioconductor website (http://bioconductor.org/packages/FunChIP). marco.morelli@iit.it. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

A laser flash photolysis-resonance fluorescence kinetics study of the reaction Cl/2P/ + CH4 yields CH3 + HCl

NASA Technical Reports Server (NTRS)

Ravishankara, A. R.; Wine, P. H.

1980-01-01

The technique of laser flash photolysis-resonance fluorescence is employed to study the kinetics of the reaction Cl(2P) + CH4 yields CH3 + HCl over the temperature range 221-375 K. At temperatures less than or equal to 241 K the apparent bimolecular rate constant is found to be dependent upon the identity of the chemically inert gases in the reaction mixture. For Cl2/CH4/He reaction mixtures (total pressure = 50 torr) different bimolecular rate constants are measured at low and high methane concentrations. For Cl2/CH4/CCl/He and Cl2/CH4/Ar reaction mixtures, the bimolecular rate constant is independent of methane concentration, being approximately equal to the rate constant measured at low methane concentrations for Cl2/CH4/He mixtures. These rate constants are in good agreement with previous results obtained using the discharge flow-resonance fluorescence and competitive chlorination techniques. At 298 K the measured bimolecular rate constant is independent of the identity of the chemically inert gases in the reaction mixture and in good agreement with all previous investigations. The low-temperature results obtained in this investigation and all previous investigations can be rationalized in terms of a model which assumes that the Cl(2P 1/2) state reacts with CH4 much faster than the Cl(2P 3/2) state. Extrapolation of this model to higher temperatures, however, is not straightforward.

The ChArMEx database

NASA Astrophysics Data System (ADS)

Ferré, Hélène; Descloitres, Jacques; Fleury, Laurence; Boichard, Jean-Luc; Brissebrat, Guillaume; Focsa, Loredana; Henriot, Nicolas; Mastrorillo, Laurence; Mière, Arnaud; Vermeulen, Anne

2013-04-01

The Chemistry-Aerosol Mediterranean Experiment (ChArMEx, http://charmex.lsce.ipsl.fr/) aims at a scientific assessment of the present and future state of the atmospheric environment in the Mediterranean Basin, and of its impacts on the regional climate, air quality, and marine biogeochemistry. The project includes long term monitoring of environmental parameters, intensive field campaigns, use of satellite data and modelling studies. Therefore ChARMEx scientists produce and need to access a wide diversity of data. In this context, the objective of the database task is to organize data management, distribution system and services such as facilitating the exchange of information and stimulating the collaboration between researchers within the ChArMEx community, and beyond. The database relies on a strong collaboration between OMP and ICARE data centres and falls within the scope of the Mediterranean Integrated Studies at Regional And Locals Scales (MISTRALS) program data portal. All the data produced by or of interest for the ChArMEx community will be documented in the data catalogue and accessible through the database website: http://mistrals.sedoo.fr/ChArMEx. The database website offers different tools: - A registration procedure which enables any scientist to accept the data policy and apply for a user database account. - Forms to document observations or products that will be provided to the database in compliance with metadata international standards (ISO 19115-19139; INSPIRE; Global Change Master Directory Thesaurus). - A search tool to browse the catalogue using thematic, geographic and/or temporal criteria. - Sorted lists of the datasets by thematic keywords, by measured parameters, by instruments or by platform type. - A shopping-cart web interface to order in situ data files. At present datasets from the background monitoring station of Ersa, Cape Corsica and from the 2012 ChArMEx pre-campaign are available. - A user-friendly access to satellite products

Photolysis of CH{sub 3}CHO at 248 nm: Evidence of triple fragmentation from primary quantum yield of CH{sub 3} and HCO radicals and H atoms

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

Morajkar, Pranay; Schoemaecker, Coralie; Fittschen, Christa, E-mail: christa.fittschen@univ-lille1.fr

2014-06-07

Radical quantum yields have been measured following the 248 nm photolysis of acetaldehyde, CH{sub 3}CHO. HCO radical and H atom yields have been quantified by time resolved continuous wave Cavity Ring Down Spectroscopy in the near infrared following their conversion to HO{sub 2} radicals by reaction with O{sub 2}. The CH{sub 3} radical yield has been determined using the same technique following their conversion into CH{sub 3}O{sub 2}. Absolute yields have been deduced for HCO radicals and H atoms through fitting of time resolved HO{sub 2} profiles, obtained under various O{sub 2} concentrations, to a complex model, while the CH{submore » 3} yield has been determined relative to the CH{sub 3} yield from 248 nm photolysis of CH{sub 3}I. Time resolved HO{sub 2} profiles under very low O{sub 2} concentrations suggest that another unknown HO{sub 2} forming reaction path exists in this reaction system besides the conversion of HCO radicals and H atoms by reaction with O{sub 2}. HO{sub 2} profiles can be well reproduced under a large range of experimental conditions with the following quantum yields: CH{sub 3}CHO + hν{sub 248nm} → CH{sub 3}CHO{sup *}, CH{sub 3}CHO{sup *} → CH{sub 3} + HCO ϕ{sub 1a} = 0.125 ± 0.03, CH{sub 3}CHO{sup *} → CH{sub 3} + H + CO ϕ{sub 1e} = 0.205 ± 0.04, CH{sub 3}CHO{sup *}→{sup o{sub 2}}CH{sub 3}CO + HO{sub 2} ϕ{sub 1f} = 0.07 ± 0.01. The CH{sub 3}O{sub 2} quantum yield has been determined in separate experiments as ϕ{sub CH{sub 3}} = 0.33 ± 0.03 and is in excellent agreement with the CH{sub 3} yields derived from the HO{sub 2} measurements considering that the triple fragmentation (R1e) is an important reaction path in the 248 nm photolysis of CH{sub 3}CHO. From arithmetic considerations taking into account the HO{sub 2} and CH{sub 3} measurements we deduce a remaining quantum yield for the molecular pathway: CH{sub 3}CHO{sup *} → CH{sub 4} + CO ϕ{sub 1b} = 0.6. All experiments

Atmospheric lifetimes and ozone depletion potentials of methyl bromide (CH3Br) and dibromomethane (CH2Br2)

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

Mellouki, A.; Talukdar, R.K.; Schmoltner, A.

The rate coefficients for the reactions of OH radical with CH3Br and CH2Br2 were measured as functions of temperature using the laser photolysis - laser induced fluorescence method. This data was incorporated into a semiempirical model (Solomon et al., 1992) and a 2D model to calculate the steady-state ozone depletion potentials (ODP) and atmospheri lifetimes, tau, with greatly improved accuracy as compared to earlier studies. The calculated ODPs and tau are 0.65 and 1.7 years and 0.17 and 0.41 years for CH3Br and CH2Br2, respectively, using the semiempirical model. These lifetimes agree well with those calculated using a 2D model.more » This study better quantifies the ODPs and tau of these species which are needed inputs for discussion of possible regulation of human emissions currently under international considerations. 29 refs.« less

Analysis of the heat capacity for pure CH4 and CH4/CCl4 on graphite near the melting point and calculation of the T-X phase diagram for (CH3)CCl3 + CCl4

NASA Astrophysics Data System (ADS)

Yurtseven, Hamit; Yılmaz, Aygül

2016-06-01

We study the temperature dependence of the heat capacity Cp for the pure CH4 and the coadsorbed CH4/CCl4 on graphite near the melting point. The heat capacity peaks are analyzed using the experimental data from the literature by means of the power-law formula. The critical exponents for the heat capacity are deduced below and above the melting point for CH4 (Tm = 104.8 K) and CH4/CCl4 (Tm = 99.2 K). Our exponent values are larger as compared with the predicted values of some theoretical models exhibiting second order transition. Our analyses indicate that the pure methane shows a nearly second order (weak discontinuity in the heat capacity peak), whereas the transition in coadsorbed CH4/CCl4 is of first order (apparent discontinuity in Cp). We also study the T - X phase diagram of a two-component system of CH3CCl3+CCl4 using the Landau phenomenological model. Phase lines of the R+L (rhombohedral+liquid) and FCC+L (face-centred cubic + liquid) are calculated using the observed T - X phase diagram of this binary mixture. Our results show that the Landau mean field theory describes the observed behavior of CH3CCl3+CCl4 adequately. From the calculated T - X phase diagram, critical behavior of some thermodynamic quantities can be predicted at various temperatures and concentrations (CCl4) for a binary mixture of CH3CCl3+CCl4.

Computational Studies Of Chemical Reactions: The Hnc-Hcn And Ch[subscript3]Nc-Ch[subscript3]Cn Isomerizations

ERIC Educational Resources Information Center

Halpern, Arthur M.

2006-01-01

The application of computational methods to the isomerization of hydrogen isocyanide to hydrogen cyanide, HNC-HCN is described. The logical extension to the exercise is presented to the isomerization of the methyl-substituted compounds, methylisocyanide and methylcyanide, Ch[subscript 3]NC-CH[subscript3]CN.

34 CFR 33.34 - Evidence.

Code of Federal Regulations, 2010 CFR

2010-07-01

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Synthesis, characterization, structural and biological aspects of copper(II) dithiocarbamate complexes - Part II, [Cu{S2CN(Me)(R1)}2], [Cu{S2CN(Me)(R2)}2] and [Cu{S2CN(R3)(R4)}2] {R1 = CH2CH(OMe)2, R2 = 2-methyl-1,3-dioxolane, R3 = CH2(CH2)2NCHPhOCH2Ph and R4 = CH2CH2OH}

NASA Astrophysics Data System (ADS)

Ferreira, Isabella P.; de Lima, Geraldo M.; Paniago, Eucler B.; Takahashi, Jacqueline A.; Krambrock, Klaus; Pinheiro, Carlos B.; Wardell, James L.; Visentin, Lorenzo C.

2013-09-01

Three new copper(II) dithiocarbamates (DTC), [Cu{S2CN(Me)(R1)}2] (1), [Cu{S2CN(Me)(R2)}2] (2) and [Cu{S2CN(R3)(R4)}2] (3) with R1 = CH2CH(OMe)2, R2 = 2-methyl-1,3-dioxolane, R3 = CH2(CH2)2NCHPhOCH2Ph and R4 = CH2CH2OH, have been synthesized and characterized by different spectroscopic techniques. Complexes (1) and (2) display typical EPR spectra for separated Cu(II) centers, and the spectrum of (3) is characteristic of two magnetically coupled Cu(II) ions with S = 1. The X-ray crystallographic determination has shown that complexes (1) and (2) crystallise in the triclinic and monoclinic systems. In addition both complexes are monomers in which the geometry at each Cu(II) is square planar. The in vitro antimicrobial activity of the sodium salts of ligands, and of the Cu(II)-DTC complexes have been screened against Aspergillus flavus, Aspergillus niger, Aspergillus parasiticus, Penicillium citrinum and Curvularia senegalensis, as well as Gram positive and Gram negative bacteria. Finally, the toxic effects of complexes (1)-(3) were performed using Chlorella vulgaris.

The Relative Abundances of Resolved 12CH2D2 and 13CH3D and Mechanisms Controlling Isotopic Bond Ordering in Abiotic and Biotic Methane Gases

NASA Astrophysics Data System (ADS)

Young, E. D.; Kohl, I. E.; Sherwood Lollar, B.; Etiope, G.; Rumble, D.; Li, S.; Haghnegahdar, M. A.; Schauble, E. A.; McCain, K.; Foustoukos, D.; Sutcliffe, C. N.; Warr, O.; Ballentine, C. J.; Onstott, T. C.; Hosgormez, H.; Neubeck, A.; Marques, J. M.; Perez-Rodriguez, I. M.; Rowe, A. R.; LaRowe, D.; Magnabosco, C.; Bryndzia, T.

2016-12-01

We report measurements of resolved 12CH2D2 and 13CH3D at natural abundances in a variety of methane gases produced naturally and in the laboratory. The ability to resolve 12CH2D2 from 13CH3D provides unprecedented insights into the origin and evolution of CH4. The results identify conditions under which either isotopic bond order disequilibrium or equilibrium are expected. Where equilibrium obtains, concordant Δ12CH2D2 and Δ13CH3D temperatures can be used reliably for thermometry. We find that concordant temperatures do not always match previous hypotheses based on indirect estimates of temperature of formation nor temperatures derived from CH4/H2 D/H exchange, underscoring the importance of reliable thermometry based on the CH4 molecules themselves. Where Δ12CH2D2 and Δ13CH3D values are inconsistent with thermodynamic equilibrium, temperatures of formation derived from these species are spurious. In such situations, while formation temperatures are unavailable, disequilibrium isotopologue ratios nonetheless provide important information about the formation mechanism of the gas and the presence or absence of multiple sources or sinks. In particular, disequilibrium isotopologue ratios may provide the means for differentiating between methane produced by abiotic synthesis versus biological processes. Deficits in 12CH2D2 compared with equilibrium values in CH4 gas made by surface-catalyzed abiotic reactions are so large as to point towards a quantum tunneling origin. Tunneling also accounts for the more moderate depletions in 13CH3D that accompany the low 12CH2D2 abundances produced by abiotic reactions. The tunneling signature of abiotic CH4 formation may prove to be an important tracer of abiotic methane formation, especially where it is preserved by dissolution of gas in cool hydrothermal systems (e.g., Mars). Isotopologue signatures of abiotic methane production can be erased by infiltration of microbial communities, and Δ12CH2D2 values are a key tracer of

iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

PubMed

Yang, Chia-Chun; Andrews, Erik H; Chen, Min-Hsuan; Wang, Wan-Yu; Chen, Jeremy J W; Gerstein, Mark; Liu, Chun-Chi; Cheng, Chao

2016-08-12

Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors (TFs). We have previously developed a probabilistic method, called TIP (Target Identification from Profiles), to identify TF target genes using ChIP-seq/ChIP-chip data. To achieve high specificity, TIP applies a conservative method to estimate significance of target genes, with the trade-off being a relatively low sensitivity of target gene identification compared to other methods. Additionally, TIP's output does not render binding-peak locations or intensity, information highly useful for visualization and general experimental biological use, while the variability of ChIP-seq/ChIP-chip file formats has made input into TIP more difficult than desired. To improve upon these facets, here we present are fined TIP with key extensions. First, it implements a Gaussian mixture model for p-value estimation, increasing target gene identification sensitivity and more accurately capturing the shape of TF binding profile distributions. Second, it enables the incorporation of TF binding-peak data by identifying their locations in significant target gene promoter regions and quantifies their strengths. Finally, for full ease of implementation we have incorporated it into a web server ( http://syslab3.nchu.edu.tw/iTAR/ ) that enables flexibility of input file format, can be used across multiple species and genome assembly versions, and is freely available for public use. The web server additionally performs GO enrichment analysis for the identified target genes to reveal the potential function of the corresponding TF. The iTAR web server provides a user-friendly interface and supports target gene identification in seven species, ranging from yeast to human. To facilitate investigating the quality of ChIP-seq/ChIP-chip data, the web server generates the chart of the

a Theoretical Characterization of Electronic States of CH2IOO and CH2OO Radicals Relevant to the Near IR Region

NASA Astrophysics Data System (ADS)

Dawes, Richard; Lolur, Phalgun; Huang, Meng; Kline, Neal; Miller, Terry A.

2015-06-01

Criegee intermediates (R1R2COO or CIs) arise from ozonolysis of biogenic and anthropogenic alkenes, which is an important process in the atmosphere. Recent breakthroughs in producing them in the gas phase have resulted in a flurry of experimental and theoretical studies. Producing the simplest CI (CH2OO) in the lab via photolysis of CH2I2 in the presence of O2 yields both CH2OO and CH2IOO with pressure dependent branching. As discussed in the preceding talk, both species might be expected to have electronic transitions in the near IR (NIR). Here we discuss electronic structure calculations used to characterize the electronic states of both systems in the relevant energy range. Using explicitly-correlated multireference configuration interaction (MRCI-F12) and coupled-cluster (UCCSD(T)-F12b) calculations we were first able to exclude CH2OO as the carrier of the observed NIR spectrum. Next, by computing frequencies and relaxed full torsional scans for the ~A and ~X states, we were able to aid in analysis and assignment of the NIR spectrum attributed to CH2IOO.

Theoretical study on the reaction mechanism of CH 4 with CaO

NASA Astrophysics Data System (ADS)

Yang, Hua-Qing; Hu, Chang-Wei; Qin, Song

2006-11-01

The reaction pathways and energetics for the reaction of methane with CaO are discussed on the singlet spin state potential energy surface at the B3LYP/6-311+G(2df,2p) and QCISD/6-311++G(3df,3pd)//B3LYP/6-311+G(2df,2p) levels of theory. The reaction of methane with CaO is proposed to proceed in the following reaction pathways: CaO + CH 4 → CaOCH 4 → [TS] → CaOH + CH 3, CaO + CH 4 → OCaCH 4 → [TS] → HOCaCH 3 → CaOH + CH 3 or [TS] → CaCH 3OH → Ca + CH 3OH, and OCaCH 4 → [TS] → HCaOCH 3 → CaOCH 3 + H or [TS] → CaCH 3OH → Ca + CH 3OH. The gas-phase methane-methanol conversion by CaO is suggested to proceed via two kinds of important reaction intermediates, HOCaCH 3 and HCaOCH 3, and the reaction pathway via the hydroxy intermediate (HOCaCH 3) is energetically more favorable than the other one via the methoxy intermediate (HCaOCH 3). The hydroxy intermediate HOCaCH 3 is predicted to be the energetically most preferred configuration in the reaction of CaO + CH 4. Meanwhile, these three product channels (CaOH + CH 3, CaOCH 3 + H and Ca + CH 3OH) are expected to compete with each other, and the formation of methyl radical is the most preferable pathway energetically. On the other hand, the intermediates HCaOCH 3 and HOCaCH 3 are predicted to be the energetically preferred configuration in the reaction of Ca + CH 3OH, which is precisely the reverse reaction of methane hydroxylation.

Detection of ethylene glycol - toward W51/e2 and G34.3+0.02

NASA Astrophysics Data System (ADS)

Lykke, Julie M.; Favre, Cécile

2014-07-01

Ethylene glycol (HOCH2CH2OH), also commenly known as antifreeze, is the reduced alcohol version of glycolaldehyde (CH2OHCHO). Glycoladehyde - the simplest possible aldehyde sugar (Marstokk and Møllendal 1973) - is the first intermediate step in the path toward forming more complex and biologically relevant molecules through the the formose reaction, which begins with formaldehyde (H2CO) and ends with the formation of sugars and ultimately ribose, the backbone of RNA (e.g., Larralde et al. 1995). The presence of glycolaldehyde is therefore an important indication that processes leading to biologically relevant molecules are taking place. It is however, still unclear as to how glycolaldehyde and ethylene glycol are formed in the ISM. It has been proposed that they share a common formation pathway through UV-irradiation of methanol (CH3OH) ices mixed with CO (Öberg et al. 2009). So far, ethylene glycol, in its lower energy con-former (g’Ga(CH2OH)2), has been detected toward SgrB2 (N) by Hollis et al. (2002), tentatively toward IRAS 16293-2422 (Jørgensen et al. 2012) and marginally by Kalenskii and Johansson (2010) toward W51 e1/e2. Here we present a firm detection of ethylene glycol toward W51/e2 as well as a first detection toward G34.3+0.02 at 1mm and 3mm using the IRAM 30m telescope.

Tree CH4 fluxes in forestry drained peatland in southern Finland

NASA Astrophysics Data System (ADS)

Haikarainen, Iikka; Putkinen, Anuliina; Pyykkö, Petteri; Halmeenmäki, Elisa; Pihlatie, Mari

2017-04-01

Methane (CH4) is among the most important greenhouse gases and its atmospheric concentration is increasing. Boreal forests are commonly considered a net sink of atmospheric CH4 due to CH4 consuming bacteria in aerated soil layers. Recent studies have, however, demonstrated that trees are capable of emitting CH4 from their stems and shoots by transporting anaerobically produced CH4 from deeper soil layers to the atmosphere. Furthermore, trees may act as independent sources of CH4. We have measured tree stem CH4 exchange of boreal tree species at Lettosuo, a nutrient rich peatland forest in Tammela, southern Finland (60˚ 38' N, 23˚ 57' E), using the static chamber technique. Three species, downy birch (Betula pubescens), Norway spruce (Picea abies) and Scots pine (Pinus sylvestris), were selected under investigation as they represent common boreal tree species. Fluxes of CH4 were measured during 7.6.2016 - 17.10.2016 from in total 25 sample trees growing on two different plots: a treatment plot where all the pines were removed to raise the water table level (WTL) and a control plot. Three birches from the treatment plot were selected to measure CH4 flux variation within vertical profile of the trees. Characterization of microbial communities, quantification of methanogenic and methanotrophic functional genes, and measurements of potential CH4 production and consumption from peat profile and forest floor moss samples were also carried out to obtain insight to the CH4 flux dynamics at the studied sites. The pine removal treatment did not markedly change the average WTL, but it made the WTL more variable with frequently 10-15 cm closer to soil surface compared to the WTL on the control plot. We found small and variable CH4 emissions from the stems of trees on both of the plots, while occasional consumption of CH4 was also present. Generally the CH4 emissions were higher and more dominant at the treatment plot compared to the control plot, and the fluxes were

Raman spectroscopy measurement of CH4 gas and CH4 dissolved in water for laser remote sensing in water

NASA Astrophysics Data System (ADS)

Somekawa, Toshihiro; Fujita, Masayuki

2018-04-01

We examined the applicability of Raman spectroscopy as a laser remote sensing tool for monitoring CH4 in water. The Raman technique has already been used successfully for measurements of CO2 gas in water. In this paper, considering the spectral transmittance of water, third harmonics of Q-switched Nd:YAG laser at 355 nm (UV region) was used for detection of CH4 Raman signals. The Raman signal at 2892 cm-1 from CH4 dissolved in water was detected at a tail of water Raman signal.

Changing concentrations of CO, CH(4), C(5)H(8), CH(3)Br, CH(3)I, and dimethyl sulfide during the Southern Ocean Iron Enrichment Experiments.

PubMed

Wingenter, Oliver W; Haase, Karl B; Strutton, Peter; Friederich, Gernot; Meinardi, Simone; Blake, Donald R; Rowland, F Sherwood

2004-06-08

Oceanic iron (Fe) fertilization experiments have advanced the understanding of how Fe regulates biological productivity and air-sea carbon dioxide (CO(2)) exchange. However, little is known about the production and consumption of halocarbons and other gases as a result of Fe addition. Besides metabolizing inorganic carbon, marine microorganisms produce and consume many other trace gases. Several of these gases, which individually impact global climate, stratospheric ozone concentration, or local photochemistry, have not been previously quantified during an Fe-enrichment experiment. We describe results for selected dissolved trace gases including methane (CH(4)), isoprene (C(5)H(8)), methyl bromide (CH(3)Br), dimethyl sulfide, and oxygen (O(2)), which increased subsequent to Fe fertilization, and the associated decreases in concentrations of carbon monoxide (CO), methyl iodide (CH(3)I), and CO(2) observed during the Southern Ocean Iron Enrichment Experiments.

The Drivers of the CH4 Seasonal Cycle in the Arctic and What Long-Term Observations of CH4 Imply About Trends in Arctic CH4 Fluxes

NASA Astrophysics Data System (ADS)

Sweeney, C.; Karion, A.; Bruhwiler, L.; Miller, J. B.; Wofsy, S. C.; Miller, C. E.; Chang, R. Y.; Dlugokencky, E. J.; Daube, B.; Pittman, J. V.; Dinardo, S. J.

2012-12-01

The large seasonal change in the atmospheric column for CH4 in the Arctic is driven by two dominant processes: transport of CH4 from low latitudes and surface emissions throughout the Arctic region. The NOAA ESRL Carbon Cycle Group Aircraft Program along with the NASA funded Carbon in Arctic Reservoirs Vulnerability Experiment (CARVE) have initiated an effort to better understand the factors controlling the seasonal changes in the mole fraction of CH4 in the Arctic with a multi-scale aircraft observing network in Alaska. The backbone of this network is multi-species flask sampling from 500 to 8000 masl that has been conducted every two weeks for the last 10 years over Poker Flat, AK. In addition regular profiles at the interior Alaska site at Poker Flat, NOAA has teamed up with the United States Coast Guard to make profiling flights with continuous observations of CO2, CO, CH4 and Ozone between Kodiak and Barrow every 2 weeks. More recently, CARVE has significantly added to this observational network with targeted flights focused on exploring the variability of CO2, CH4 and CO in the boundary layer both in the interior and the North Slope regions of Alaska. Taken together with the profiling of HIAPER Pole-to-Pole Observations (HIPPO), ground sites at Barrow and a new CARVE interior Alaska surface site just north of Fairbanks, AK, we now have the ability to investigate the full evolution of the seasonal cycle in the Arctic using both the multi-scale sampling offered by the different aircraft platforms as well as the multi-species sampling offered by in-situ and flask sampling. The flasks also provide a valuable tie-point between different platforms so that spatial and temporal gradients can be properly interpreted. In the context of the seasonal cycle observed by the aircraft platforms we will look at long term ground observations over the last 20 years to assess changes in Arctic CH4 emissions which have occurred as a result of 0.6C/decade changes in mean surface

How to Combine ChIP with qPCR.

PubMed

Asp, Patrik

2018-01-01

Chromatin immunoprecipitation (ChIP) coupled with quantitative PCR (qPCR) has in the last 15 years become a basic mainstream tool in genomic research. Numerous commercially available ChIP kits, qPCR kits, and real-time PCR systems allow for quick and easy analysis of virtually anything chromatin-related as long as there is an available antibody. However, the highly accurate quantitative dimension added by using qPCR to analyze ChIP samples significantly raises the bar in terms of experimental accuracy, appropriate controls, data analysis, and data presentation. This chapter will address these potential pitfalls by providing protocols and procedures that address the difficulties inherent in ChIP-qPCR assays.

The ChArMEx database

NASA Astrophysics Data System (ADS)

Ferré, Helene; Belmahfoud, Nizar; Boichard, Jean-Luc; Brissebrat, Guillaume; Descloitres, Jacques; Fleury, Laurence; Focsa, Loredana; Henriot, Nicolas; Mastrorillo, Laurence; Mière, Arnaud; Vermeulen, Anne

2014-05-01

The Chemistry-Aerosol Mediterranean Experiment (ChArMEx, http://charmex.lsce.ipsl.fr/) aims at a scientific assessment of the present and future state of the atmospheric environment in the Mediterranean Basin, and of its impacts on the regional climate, air quality, and marine biogeochemistry. The project includes long term monitoring of environmental parameters, intensive field campaigns, use of satellite data and modelling studies. Therefore ChARMEx scientists produce and need to access a wide diversity of data. In this context, the objective of the database task is to organize data management, distribution system and services, such as facilitating the exchange of information and stimulating the collaboration between researchers within the ChArMEx community, and beyond. The database relies on a strong collaboration between OMP and ICARE data centres and has been set up in the framework of the Mediterranean Integrated Studies at Regional And Locals Scales (MISTRALS) program data portal. All the data produced by or of interest for the ChArMEx community will be documented in the data catalogue and accessible through the database website: http://mistrals.sedoo.fr/ChArMEx. At present, the ChArMEx database contains about 75 datasets, including 50 in situ datasets (2012 and 2013 campaigns, Ersa background monitoring station), 25 model outputs (dust model intercomparison, MEDCORDEX scenarios), and a high resolution emission inventory over the Mediterranean. Many in situ datasets have been inserted in a relational database, in order to enable more accurate data selection and download of different datasets in a shared format. The database website offers different tools: - A registration procedure which enables any scientist to accept the data policy and apply for a user database account. - A data catalogue that complies with metadata international standards (ISO 19115-19139; INSPIRE European Directive; Global Change Master Directory Thesaurus). - Metadata forms to document

Interfacial electronic structures revealed at the rubrene/CH3NH3PbI3 interface.

PubMed

Ji, Gengwu; Zheng, Guanhaojie; Zhao, Bin; Song, Fei; Zhang, Xiaonan; Shen, Kongchao; Yang, Yingguo; Xiong, Yimin; Gao, Xingyu; Cao, Liang; Qi, Dong-Chen

2017-03-01

The electronic structures of rubrene films deposited on CH 3 NH 3 PbI 3 perovskite have been investigated using in situ ultraviolet photoelectron spectroscopy (UPS) and X-ray photoelectron spectroscopy (XPS). It was found that rubrene molecules interacted weakly with the perovskite substrate. Due to charge redistribution at their interface, a downward 'band bending'-like energy shift of ∼0.3 eV and an upward band bending of ∼0.1 eV were identified at the upper rubrene side and the CH 3 NH 3 PbI 3 substrate side, respectively. After the energy level alignment was established at the rubrene/CH 3 NH 3 PbI 3 interface, its highest occupied molecular orbital (HOMO)-valence band maximum (VBM) offset was found to be as low as ∼0.1 eV favoring the hole extraction with its lowest unoccupied molecular orbital (LUMO)-conduction band minimum (CBM) offset as large as ∼1.4 eV effectively blocking the undesired electron transfer from perovskite to rubrene. As a demonstration, simple inverted planar solar cell devices incorporating rubrene and rubrene/poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) hole transport layers (HTLs) were fabricated in this work and yielded a champion power conversion efficiency of 8.76% and 13.52%, respectively. Thus, the present work suggests that a rubrene thin film could serve as a promising hole transport layer for efficient perovskite-based solar cells.

Tessellated gold nanostructures from Au144(SCH2CH2Ph)60 molecular precursors and their use in organic solar cell enhancement

NASA Astrophysics Data System (ADS)

Bauld, Reg; Hesari, Mahdi; Workentin, Mark S.; Fanchini, Giovanni

2014-06-01

We report for the first time the fabrication of nanocomposite hole-blocking layers consisting of poly-3,4-ethylene-dioxythiophene:poly-styrene-sulfonate (PEDOT:PSS) thin films incorporating networks of gold nanoparticles assembled from Au144(SCH2CH2Ph)60, a molecular gold precursor. These thin films can be prepared reproducibly on indium tin oxide by spinning on it Au144(SCH2CH2Ph)60 solutions in chlorobenzene, annealing the resulting thin film at 400 °C, and subsequently spinning PEDOT:PSS on top. The use of our nanocomposite hole-blocking layers for enhancing the photoconversion efficiency of bulk heterojunction organic solar cells is demonstrated. By varying the concentration of Au144(SCH2CH2Ph)60 in the starting solution and the annealing time, different gold nanostructures were obtained ranging from individual gold nanoparticles (AuNPs) to tessellated networks of gold nanostructures (Tess-AuNPs). Improvement in organic solar cell efficiencies up to 10% relative to a reference cell is demonstrated with Tess-AuNPs embedded in PEDOT:PSS.

Crystal structure of the DNA-binding domain of the LysR-type transcriptional regulator CbnR in complex with a DNA fragment of the recognition-binding site in the promoter region.

PubMed

Koentjoro, Maharani Pertiwi; Adachi, Naruhiko; Senda, Miki; Ogawa, Naoto; Senda, Toshiya

2018-03-01

LysR-type transcriptional regulators (LTTRs) are among the most abundant transcriptional regulators in bacteria. CbnR is an LTTR derived from Cupriavidus necator (formerly Alcaligenes eutrophus or Ralstonia eutropha) NH9 and is involved in transcriptional activation of the cbnABCD genes encoding chlorocatechol degradative enzymes. CbnR interacts with a cbnA promoter region of approximately 60 bp in length that contains the recognition-binding site (RBS) and activation-binding site (ABS). Upon inducer binding, CbnR seems to undergo conformational changes, leading to the activation of the transcription. Since the interaction of an LTTR with RBS is considered to be the first step of the transcriptional activation, the CbnR-RBS interaction is responsible for the selectivity of the promoter to be activated. To understand the sequence selectivity of CbnR, we determined the crystal structure of the DNA-binding domain of CbnR in complex with RBS of the cbnA promoter at 2.55 Å resolution. The crystal structure revealed details of the interactions between the DNA-binding domain and the promoter DNA. A comparison with the previously reported crystal structure of the DNA-binding domain of BenM in complex with its cognate RBS showed several differences in the DNA interactions, despite the structural similarity between CbnR and BenM. These differences explain the observed promoter sequence selectivity between CbnR and BenM. Particularly, the difference between Thr33 in CbnR and Ser33 in BenM appears to affect the conformations of neighboring residues, leading to the selective interactions with DNA. Atomic coordinates and structure factors for the DNA-binding domain of Cupriavidus necatorNH9 CbnR in complex with RBS are available in the Protein Data Bank under the accession code 5XXP. © 2018 Federation of European Biochemical Societies.

Production of bioplastics and hydrogen gas by photosynthetic microorganisms

NASA Astrophysics Data System (ADS)

Yasuo, Asada; Masato, Miyake; Jun, Miyake

1998-03-01

Our efforts have been aimed at the technological basis of photosynthetic-microbial production of materials and an energy carrier. We report here accumulation of poly-(3-hydroxybutyrate) (PHB), a raw material of biodegradable plastics and for production of hydrogen gas, and a renewable energy carrier by photosynthetic microorganisms (tentatively defined as cyanobacteria plus photosynthetic bateria, in this report). A thermophilic cyanobacterium, Synechococcus sp. MA19 that accumulates PHB at more than 20% of cell dry wt under nitrogen-starved conditions was isolated and microbiologically identified. The mechanism of PHB accumulation was studied. A mesophilic Synechococcus PCC7942 was transformed with the genes encoding PHB-synthesizing enzymes from Alcaligenes eutrophus. The transformant accumulated PHB under nitrogen-starved conditions. The optimal conditions for PHB accumulation by a photosynthetic bacterium grown on acetate were studied. Hydrogen production by photosynthetic microorganisms was studied. Cyanobacteria can produce hydrogen gas by nitrogenase or hydrogenase. Hydrogen production mediated by native hydrogenase in cyanobacteria was revealed to be in the dark anaerobic degradation of intracellular glycogen. A new system for light-dependent hydrogen production was targeted. In vitro and in vivo coupling of cyanobacterial ferredoxin with a heterologous hydrogenase was shown to produce hydrogen under light conditions. A trial for genetic trasformation of Synechococcus PCC7942 with the hydrogenase gene from Clostridium pasteurianum is going on. The strong hydrogen producers among photosynthetic bacteria were isolated and characterized. Co-culture of Rhodobacter and Clostriumdium was applied to produce hydrogen from glucose. Conversely in the case of cyanobacteria, genetic regulation of photosynthetic proteins was intended to improve conversion efficiency in hydrogen production by the photosynthetic bacterium, Rhodobacter sphaeroides RV. A mutant acquired by

Phase Equilibria and Transport Properties in the Systems AgNO3/RCN/H2O. R = CH3, C2H5, C3H7, C4H,, C6H5, and C6H5CH2

NASA Astrophysics Data System (ADS)

Das, Surjya P.; Wittekopf, Burghard; Weil, Konrad G.

1988-11-01

Silver nitrate can form homogeneous liquid phases with some organic nitriles and water, even when there is no miscibility between the pure liquid components. We determined the shapes of the single phase regions in the ternary phase diagram for the following systems: silver nitrate /RCN /H2O with R =CH3, C3H7, C6H5, and C6H5CH2 at room temperature and for R =C6H5 also at 60 °C and O °C. Furthermore we studied kinematic viscosities, electrical conductivities, and densities of mixtures containing silver nitrate, RCN, and water with the mole ratios X /4 /1 (0.2≦ X ≦S 3.4). In these cases also R = C2H5 and C4H9 were studied. The organic nitriles show different dependences of viscosity and conductivity on the silver nitrate content from the aliphatic ones.

Rate coefficients for the gas-phase reaction of the hydroxyl radical with CH2=CHF and CH2=CF2.

PubMed

Baasandorj, Munkhbayar; Knight, Gary; Papadimitriou, Vassileios C; Talukdar, Ranajit K; Ravishankara, A R; Burkholder, James B

2010-04-08

Rate coefficients, k, for the gas-phase reaction of the OH radical with CH(2)=CHF (k(1)) and CH(2)=CF(2) (k(2)) were measured under pseudo-first-order conditions in OH using pulsed laser photolysis to produce OH and laser-induced fluorescence (PLP-LIF) to detect it. Rate coefficients were measured over a range of temperature (220-373 K) and bath gas pressure (20-600 Torr; He, N(2)). The rate coefficients were found to be independent of pressure. The measured rate coefficient for reaction 1 at room temperature was k(1)(296 K) = (5.18 +/- 0.50) x 10(-12) cm(3) molecule(-1) s(-1), independent of pressure, and the temperature dependence is given by the Arrhenius expression k(1)(T) = (1.75 +/- 0.20) x 10(-12) exp[(316 +/- 25)/T] cm(3) molecule(-1) s(-1); the rate coefficients for reaction 2 were k(2)(296 K) = (2.79 +/- 0.25) x 10(-12) cm(3) molecule(-1) s(-1) and k(2)(T) = (1.75 +/- 0.20) x 10(-12) exp[(140 +/- 20)/T] cm(3) molecule(-1) s(-1). The quoted uncertainties are 2sigma (95% confidence level) and include estimated systematic errors. The fall-off parameters for reaction 2 of k(infinity) = 3 x 10(-12) cm(3) molecule(-1) s(-1) and k(0)(296 K) = 1.8 x 10(-28) cm(6) molecule(-2) s(-1) with F(c) = 0.6 reproduce the room temperature data obtained in this study combined with the low pressure rate coefficient data from Howard (J. Chem. Phys. 1976, 65, 4771). OH radical formation was observed for reactions 1 and 2 in the presence of O(2), and the mechanism was investigated using (18)OH and OD rate coefficient measurements with CH(2)=CHF and CH(2)=CF(2) over a range of temperature (260-373 K) and pressure (20-100 Torr, He). Quantum chemical calculations using density functional theory (DFT) were used to determine the geometries and energies of the reactants and adducts formed in reactions 1 and 2 and the peroxy radicals formed following the addition of O(2). The atmospheric lifetimes of CH(2)=CHF and CH(2)=CF(2) due to loss by reaction with OH are approximately 2 and 4

Chemical and isotopic equilibrium between CO 2 and CH 4 in fumarolic gas discharges: Generation of CH 4 in arc magmatic-hydrothermal systems

NASA Astrophysics Data System (ADS)

Fiebig, Jens; Chiodini, Giovanni; Caliro, Stefano; Rizzo, Andrea; Spangenberg, Jorge; Hunziker, Johannes C.

2004-05-01

The chemical and isotopic composition of fumarolic gases emitted from Nisyros Volcano, Greece, and of a single gas sample from Vesuvio, Italy, was investigated in order to determine the origin of methane (CH 4) within two subduction-related magmatic-hydrothermal environments. Apparent temperatures derived from carbon isotope partitioning between CH 4 and CO 2 of around 340°C for Nisyros and 470°C for Vesuvio correlate well with aquifer temperatures as measured directly and/or inferred from compositional data using the H 2O-H 2-CO 2-CO-CH 4 geothermometer. Thermodynamic modeling reveals chemical equilibrium between CH 4, CO 2 and H 2O implying that carbon isotope partitioning between CO 2 and CH 4 in both systems is controlled by aquifer temperature. N 2/ 3He and CH 4/ 3He ratios of Nisyros fumarolic gases are unusually low for subduction zone gases and correspond to those of midoceanic ridge environments. Accordingly, CH 4 may have been primarily generated through the reduction of CO 2 by H 2 in the absence of any organic matter following a Fischer-Tropsch-type reaction. However, primary occurrence of minor amounts of thermogenic CH 4 and subsequent re-equilibration with co-existing CO 2 cannot be ruled out entirely. CO 2/ 3He ratios and δ 13C CO 2 values imply that the evolved CO 2 either derives from a metasomatized mantle or is a mixture between two components, one outgassing from an unaltered mantle and the other released by thermal breakdown of marine carbonates. The latter may contain traces of organic matter possibly decomposing to CH 4 during thermometamorphism.

The First Laboratory Detection of Vibration-rotation Transitions of 12CH+ and 13CH+ and Improved Measurement of Their Rotational Transition Frequencies

NASA Astrophysics Data System (ADS)

Doménech, José L.; Jusko, Pavol; Schlemmer, Stephan; Asvany, Oskar

2018-04-01

C–H stretches of the fundamental ions CH+ and 13CH+, which have long been searched for, have been observed for the first time in the laboratory. The state-dependent attachment of He atoms to these ions at cryogenic temperatures has been exploited to obtain high-resolution rovibrational data. In addition, the lowest rotational transitions of CH+, 13CH+ and CD+ have been revisited and their rest frequency values have improved substantially.

G331.512–0.103: An Interstellar Laboratory for Molecular Synthesis. I. The Ortho-to-para Ratios for CH3OH and CH3CN

NASA Astrophysics Data System (ADS)

Mendoza, Edgar; Bronfman, Leonardo; Duronea, Nicolas U.; Lépine, Jacques R. D.; Finger, Ricardo; Merello, Manuel; Hervías-Caimapo, Carlos; Gama, Diana R. G.; Reyes, Nicolas; Åke-Nyman, Lars

2018-02-01

Spectral line surveys reveal rich molecular reservoirs in G331.512–0.103, a compact radio source in the center of an energetic molecular outflow. In this first work, we analyze the physical conditions of the source by means of CH3OH and CH3CN. The observations were performed with the APEX Telescope. Six different system configurations were defined to cover most of the band within (292–356) GHz as a consequence, we detected a forest of lines toward the central core. A total of 70 lines of A/E–CH3OH and A/E–CH3CN were analyzed, including torsionally excited transitions of CH3OH ({ν }t=1). In a search for all the isotopologues, we identified transitions of 13CH3OH. The physical conditions were derived considering collisional and radiative processes. We found common temperatures for each A and E symmetry of CH3OH and CH3CN; the derived column densities indicate an A/E equilibrated ratio for both tracers. The results reveal that CH3CN and CH3OH trace a hot and cold component with {T}k∼ 141 K and {T}k∼ 74 K, respectively. In agreement with previous ALMA observations, the models show that the emission region is compact (≲ 5\\buildrel{\\prime\\prime}\\over{.} 5) with gas density n(H2) = (0.7–1)×107 cm‑3. The CH3OH/CH3CN abundance ratio and the evidences for prebiotic and complex organic molecules suggest a rich and active chemistry toward G331.512–0.103.

A new method for speciated CH3O2 radical detection and HIRAC (Highly Instrumented Reactor for Atmospheric Chemistry) studies of the CH3O2 self-reaction

NASA Astrophysics Data System (ADS)

Onel, Lavinia; Brennan, Alexander; Seakins, Paul W.; Whalley, Lisa; Heard, Dwayne

2016-04-01

A new method has been developed for the speciated detection of CH3O2 radicals by FAGE (Fluorescence Assay by Gas Expansion) by titrating CH3O2 to CH3O by reaction with added NO and then detecting the resultant CH3O by LIF (laser induced fluorescence). The limit of detection of the technique is ˜108 cm-3 CH3O2 for a unity signal-to-noise ratio and 5 min averaging time. The method has been used for time monitoring of CH3O2 during its self-reaction within HIRAC at 1 bar and room temperature to determine a preliminary value of the rate coefficient of 4.2 × 10-13 cm3 s-1, which lies in the range of the previous results, (2.7 - 5.2) × 10-13 cm3 s-1.1 In addition to detection of CH3O2, products of the CH3O2 self-reaction were also observed for the two reaction channels over a range of temperatures from 260 - 320 K: (a) 2CH3O2 → CH2O + CH3OH; (b) 2CH3O2 → 2CH3O + O2, namely HO2 radicals (from reaction of CH3O + O2) and formaldehyde monitored by FAGE and formaldehyde and methanol observed by FTIR. A good agreement has been obtained between the FTIR and FAGE measurements of CH2O which increased to ˜ 2 ppmv over the experiments. Using the concentrations of CH3OH and CH2O, the branching ratio for channel (a) at room temperature has been determined as ra = 0.66 ± 0.06. The result is in very good agreement with the value recommended in the review of Tyndall et al.2 of ra = 0.63 ± 0.06. No temperature dependence of ra has been observed from 296 K to 321 K. 1. http://iupac.pole-ether.fr/ 2. G. S. Tyndall et al., J. Geophys. Res. 106, 12157 (2001).

Crystal and molecular structure of the first dibino non-geminal macrocyclic dicyclophosphazene, & {;N 3P 3Cl 4[HN(CH 2) 3O(CH 2) 2O(CH 2) 3NH]&}; 2

NASA Astrophysics Data System (ADS)

Enjalbert, Renée; Galy, Jean; Sournies, François; Labarre, Jean-François

1990-04-01

Reaction of N 3P 3Cl 6 with the 4,7-dioxadecane-1,10-diamine (coded as 3O2O3) using an Et 2O/Na 2CO 3 water interface process leads to the DIBINO non-geminal 30-membered macrocyclic dicyclophosphazene &{;N 3P 3Cl 4[HN(CH 2) 3O(CH 2) 2O(CH 2) 3NH]&}; 2. This 30-crown-ether-like architecture crystallizes in the triclinic system, P1, a=9.019(6), b=9.224(5), c=11.542(8) Å, α=94.87(4), β=95.97(4), γ=99.68(3)°, V=936(1) Å 3, Dx=1.599 Mg m -3, R=0.049 for 2862 unique reflections and 199 variable parameters. The structure exhibits a spatial arrangement of two N 3P 3Cl 4 with two [HN(CH 2) 3O(CH 2) 3O(CH 2) 3NH] as bridges on different P atoms of N 3P 3 rings. Moreover, the two N 3P 3 rings are trans to the average plane of the 30-membered macrocycle ("chair" conformation).

CO2 and CH4 emissions from streams in a lake-rich landscape: Patterns, controls, and regional significance

USGS Publications Warehouse

Crawford, John T.; Lottig, Noah R.; Stanley, Emily H.; Walker, John F.; Hanson, Paul C.; Finlay, Jacques C.; Striegl, Robert G.

2014-01-01

Aquatic ecosystems are important components of landscape carbon budgets. In lake-rich landscapes, both lakes and streams may be important sources of carbon gases (CO2 and CH4) to the atmosphere, but the processes that control gas concentrations and emissions in these interconnected landscapes have not been adequately addressed. We use multiple data sets that vary in their spatial and temporal extent during 2001–2012 to investigate the carbon gas source strength of streams in a lake-rich landscape and to determine the contribution of lakes, metabolism, and groundwater to stream CO2 and CH4. We show that streams emit roughly the same mass of CO2 (23.4 Gg C yr−1; 0.49 mol CO2 m−2 d−1) as lakes at a regional scale (27 Gg C yr−1) and that stream CH4 emissions (189 Mg C yr−1; 8.46 mmol CH4 m−2 d−1) are an important component of the regional greenhouse gas balance. Gas transfer velocity variability (range = 0.34 to 13.5 m d−1) contributed to the variability of gas flux in this landscape. Groundwater inputs and in-stream metabolism control stream gas supersaturation at the landscape scale, while carbon cycling in lakes and deep groundwaters does not control downstream gas emissions. Our results indicate the need to consider connectivity of all aquatic ecosystems (lakes, streams, wetlands, and groundwater) in lake-rich landscapes and their connections with the terrestrial environment in order to understand the full nature of the carbon cycle.

Coupled potential energy surface for the F(2P)+CH4→HF+CH3 entrance channel and quantum dynamics of the CH4·F- photodetachment.

PubMed

Westermann, Till; Eisfeld, Wolfgang; Manthe, Uwe

2013-07-07

An approach to construct vibronically and spin-orbit coupled diabatic potential energy surfaces (PESs) which describe all three relevant electronic states in the entrance channels of the X(P) + CH4 →HX + CH3 reactions (with X=F((2)P), Cl((2)P), or O((3)P)) is introduced. The diabatization relies on the permutational symmetry present in the methane molecule and results in diabatic states which transform as the three p orbitals of the X atom. Spin-orbit coupling is easily and accurately included using the atomic spin-orbit coupling matrix of the isolated X atom. The method is applied to the F + CH4 system obtaining an accurate PES for the entrance channel based on ab initio multi-reference configuration interaction (MRCI) calculations. Comparing the resulting PESs with spin-orbit MRCI calculations, excellent agreement is found for the excited electronic states at all relevant geometries. The photodetachment spectrum of CH4·F(-) is investigated via full-dimensional (12D) quantum dynamics calculations on the coupled PESs using the multi-layer multi-configurational time-dependent Hartree approach. Extending previous work [J. Palma and U. Manthe, J. Chem. Phys. 137, 044306 (2012)], which was restricted to the dynamics on a single adiabatic PES, the contributions of the electronically excited states to the photodetachment spectrum are calculated and compared to experiment. Considering different experimental setups, good agreement between experiment and theory is found. Addressing questions raised in the previous work, the present dynamical calculations show that the main contribution to the second peak in the photodetachment spectrum results from electron detachment into the electronically excited states of the CH4F complex.

Reactivity of OH and CH3OH Between 22 and 64 K: Modelling the Gas Phase Production of CH3O in Barnard 1B

PubMed Central

Antiñolo, M.; Agúndez, M.; Jiménez, E.; Ballesteros, B.; Canosa, A.; Dib, G. El; Albaladejo, J.; Cernicharo, J.

2016-01-01

In the last years, ultra-low temperature chemical kinetic experiments have demonstrated that some gas-phase reactions are much faster than previously thought. One example is the reaction between OH and CH3OH, which has been recently found to be accelerated at low temperatures yielding CH3O as main product. This finding opened the question of whether the CH3O observed in the dense core Barnard 1b could be formed by the gas-phase reaction of CH3OH and OH. Several chemical models including this reaction and grain-surface processes have been developed to explain the observed abundance of CH3O with little success. Here we report for the first time rate coefficients for the gas-phase reaction of OH and CH3OH down to a temperature of 22 K, very close to those in cold interstellar clouds. Two independent experimental set-ups based on the supersonic gas expansion technique coupled to the pulsed laser photolysis-laser induced fluorescence technique were used to determine rate coefficients in the temperature range 22-64 K. The temperature dependence obtained in this work can be expressed as k(22-64 K) = (3.6 ± 0.1) × 10−12(T/300 K)−(1.0±0.2) cm3 molecule−1 s−1. Implementing this expression in a chemical model of a cold dense cloud results in CH3O/CH3OH abundance ratios similar or slightly lower than the value of ∼ 3 × 10−3 observed in Barnard 1b. This finding confirms that the gas-phase reaction between OH and CH3OH is an important contributor to the formation of interstellar CH3O. The role of grain-surface processes in the formation of CH3O, although it cannot be fully neglected, remains controversial. PMID:27279655

Reactivity of OH and CH3OH Between 22 and 64 K: Modelling the Gas Phase Production of CH3O in Barnard 1B.

PubMed

Antiñolo, M; Agúndez, M; Jiménez, E; Ballesteros, B; Canosa, A; Dib, G El; Albaladejo, J; Cernicharo, J

2016-05-20

In the last years, ultra-low temperature chemical kinetic experiments have demonstrated that some gas-phase reactions are much faster than previously thought. One example is the reaction between OH and CH 3 OH, which has been recently found to be accelerated at low temperatures yielding CH 3 O as main product. This finding opened the question of whether the CH 3 O observed in the dense core Barnard 1b could be formed by the gas-phase reaction of CH 3 OH and OH. Several chemical models including this reaction and grain-surface processes have been developed to explain the observed abundance of CH 3 O with little success. Here we report for the first time rate coefficients for the gas-phase reaction of OH and CH 3 OH down to a temperature of 22 K, very close to those in cold interstellar clouds. Two independent experimental set-ups based on the supersonic gas expansion technique coupled to the pulsed laser photolysis-laser induced fluorescence technique were used to determine rate coefficients in the temperature range 22-64 K. The temperature dependence obtained in this work can be expressed as k (22-64 K) = (3.6 ± 0.1) × 10 -12 ( T/ 300 K) -(1.0±0.2) cm 3 molecule -1 s -1 . Implementing this expression in a chemical model of a cold dense cloud results in CH 3 O/CH 3 OH abundance ratios similar or slightly lower than the value of ∼ 3 × 10 -3 observed in Barnard 1b. This finding confirms that the gas-phase reaction between OH and CH 3 OH is an important contributor to the formation of interstellar CH 3 O. The role of grain-surface processes in the formation of CH 3 O, although it cannot be fully neglected, remains controversial.

The Structure of Titan’s N2 and CH4 Coronae

NASA Astrophysics Data System (ADS)

Jiang, Fayu; Cui, Jun; Xu, Jiyao

2017-12-01

In this study, we analyze the structures of Titan’s N2 and CH4 coronae using a large data set acquired by the Ion Neutral Mass Spectrometer (INMS) instrument on board Cassini. The N2 and CH4 densities measured from the exobase up to 2000 km imply a mean exobase temperature of 146 K and 143 K, respectively, which is lower than the mean upper atmospheric temperature by 4 and 7 K. This indicates that on average, Titan possesses a subthermal rather than suprathermal corona. A careful examination reveals that the variability in corona structure is not very likely to be solar driven. Within the framework of the collisionless kinetic model, we investigate how the CH4 energy distribution near the exobase could be constrained if strong CH4 escape occurs on Titan. Several functional forms for the CH4 energy distribution are attempted, assuming two representative CH4 escape rates of 1.2× {10}25 s-1 and 2.2× {10}27 s-1. We find that the double Maxwellian and power-law distributions can reproduce the shape of the CH4 corona structure as well as the imposed CH4 escape rate. In both cases, the escape rate is contributed by a suprathermal CH4 population on the high-energy tail, with a number fraction below 5% and a characteristic energy of 0.1-0.6 eV per suprathermal CH4 molecule. The coexistence of the subthermal CH4 corona revealed by the INMS data and substantial CH4 escape suggested by some previous works could be reconciled by a significant departure in the exobase CH4 energy distribution from ideal Maxwellian that enhances escape and causes a noticeable redistribution of the corona structure.

The relative abundances of resolved l2CH2D2 and 13CH3D and mechanisms controlling isotopic bond ordering in abiotic and biotic methane gases

NASA Astrophysics Data System (ADS)

Young, E. D.; Kohl, I. E.; Lollar, B. Sherwood; Etiope, G.; Rumble, D.; Li, S.; Haghnegahdar, M. A.; Schauble, E. A.; McCain, K. A.; Foustoukos, D. I.; Sutclife, C.; Warr, O.; Ballentine, C. J.; Onstott, T. C.; Hosgormez, H.; Neubeck, A.; Marques, J. M.; Pérez-Rodríguez, I.; Rowe, A. R.; LaRowe, D. E.; Magnabosco, C.; Yeung, L. Y.; Ash, J. L.; Bryndzia, L. T.

2017-04-01

We report measurements of resolved 12CH2D2 and 13CH3D at natural abundances in a variety of methane gases produced naturally and in the laboratory. The ability to resolve 12CH2D2 from 13CH3D provides unprecedented insights into the origin and evolution of CH4. The results identify conditions under which either isotopic bond order disequilibrium or equilibrium are expected. Where equilibrium obtains, concordant Δ12CH2D2 and Δ13CH3D temperatures can be used reliably for thermometry. We find that concordant temperatures do not always match previous hypotheses based on indirect estimates of temperature of formation nor temperatures derived from CH4/H2 D/H exchange, underscoring the importance of reliable thermometry based on the CH4 molecules themselves. Where Δ12CH2D2 and Δ13CH3D values are inconsistent with thermodynamic equilibrium, temperatures of formation derived from these species are spurious. In such situations, while formation temperatures are unavailable, disequilibrium isotopologue ratios nonetheless provide novel information about the formation mechanism of the gas and the presence or absence of multiple sources or sinks. In particular, disequilibrium isotopologue ratios may provide the means for differentiating between methane produced by abiotic synthesis vs. biological processes. Deficits in 12CH2D2 compared with equilibrium values in CH4 gas made by surface-catalyzed abiotic reactions are so large as to point towards a quantum tunneling origin. Tunneling also accounts for the more moderate depletions in 13CH3D that accompany the low 12CH2D2 abundances produced by abiotic reactions. The tunneling signature may prove to be an important tracer of abiotic methane formation, especially where it is preserved by dissolution of gas in cool hydrothermal systems (e.g., Mars). Isotopologue signatures of abiotic methane production can be erased by infiltration of microbial communities, and Δ12CH2D2 values are a key tracer of microbial recycling.

Chromatin Immunoprecipitation (ChIP) Protocol for Low-abundance Embryonic Samples.

PubMed

Rehimi, Rizwan; Bartusel, Michaela; Solinas, Francesca; Altmüller, Janine; Rada-Iglesias, Alvaro

2017-08-29

Chromatin immunoprecipitation (ChIP) is a widely-used technique for mapping the localization of post-translationally modified histones, histone variants, transcription factors, or chromatin-modifying enzymes at a given locus or on a genome-wide scale. The combination of ChIP assays with next-generation sequencing (i.e., ChIP-Seq) is a powerful approach to globally uncover gene regulatory networks and to improve the functional annotation of genomes, especially of non-coding regulatory sequences. ChIP protocols normally require large amounts of cellular material, thus precluding the applicability of this method to investigating rare cell types or small tissue biopsies. In order to make the ChIP assay compatible with the amount of biological material that can typically be obtained in vivo during early vertebrate embryogenesis, we describe here a simplified ChIP protocol in which the number of steps required to complete the assay were reduced to minimize sample loss. This ChIP protocol has been successfully used to investigate different histone modifications in various embryonic chicken and adult mouse tissues using low to medium cell numbers (5 x 10 4 - 5 x 10 5 cells). Importantly, this protocol is compatible with ChIP-seq technology using standard library preparation methods, thus providing global epigenomic maps in highly relevant embryonic tissues.

Temperature-Dependent Kinetics Studies of the Reactions Br((sup 2)P(sub 3/2)) + CH3SCH3 reversible reaction CH3SCH2 + HBr. Heat of Formation of the CH3SCH2 Radical

NASA Technical Reports Server (NTRS)

Jefferson, A.; Nicovich, J. M.; Wine, P. H.

1997-01-01

Time-resolved resonance fluorescence detection of Br((sup 2)P(sub 3/2)) atom disappearance or appearance 266 nm laser flash photolysis of CF2Br2/CH3SCH3/H2/N2 and Cl2CO/CH2SCH3/HBr/H2/N2 mixtures has been employed to study the kinetics of the reactions Br((sup 2)P(sub 3/2)) + CH3SCH3 reversible reaction HBr + CH3SCH2 (1,-1) as a function of temperature over the range 386-604 K. Arrhenius expressions in units of cu cm/molecule which describe the results are k3= (9.0 +/- 2.9) x 10 (exp -11) exp[(-2386 +/- 151)/T]; errors are 2 sigma and represent precision only. To our knowledge, these are the first kinetic data reported for each of the two reactions studied. Second and third law analyses of the equilibrium data for reactions 1 and -1 have been employed to obtain the following enthalpies of reaction in units of kcal/mol: Delta-H(298) = 6.11 +/- 1.37 and Delta-H(0) = 5.37 +/- 1.38. Combining the above enthalpies of reaction with the well-known heats of formation of Br, HBr, CH3SCH3 gives the following heats of formation of the CH3SCH2 radical in units of kcal/mol: Delta-H(sub(f,298)) = 32.7 +/- 1.4 and Delta-H(sub (f,0)) = 35.3 +/- 1.4; errors are 2 sigma and represent estimates of absolute accuracy. The C-H bond dissociation energy in CH3SCH3 obtained from our data, 93.7 +/- 1.4 kcal/mol at 298 K and 92.0 +/- 1.4 kcal at 0 k, agrees well with a recent molecular beam photofragmentaion study but is 3 kcal/mol lower than the value obtained from an iodination kinetics study.

34 CFR 34.21 - Employer certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

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34 CFR 34.22 - Employer responsibilities.

Code of Federal Regulations, 2010 CFR

2010-07-01

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Code of Federal Regulations, 2010 CFR

2010-07-01

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Code of Federal Regulations, 2010 CFR

2010-07-01

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34 CFR 34.26 - Ending garnishment.

Code of Federal Regulations, 2010 CFR

2010-07-01

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Enhanced Performance of Perovskite CH3NH3PbI3 Solar Cell by Using CH3NH3I as Additive in Sequential Deposition.

PubMed

Xie, Yian; Shao, Feng; Wang, Yaoming; Xu, Tao; Wang, Deliang; Huang, Fuqiang

2015-06-17

Sequential deposition is a widely adopted method to prepare CH3NH3PbI3 on mesostructured TiO2 electrode for organic lead halide perovskite solar cells. However, this method often suffers from the uncontrollable crystal size, surface morphology, and residual PbI2 in the resulting CH3NH3PbI3, which are all detrimental to the device performance. We herein present an optimized sequential solution deposition method by introducing different amount of CH3NH3I in PbI2 precursor solution in the first step to prepare CH3NH3PbI3 absorber on mesoporous TiO2 substrates. The addition of CH3NH3I in PbI2 precursor solution can affect the crystallization and composition of PbI2 raw films, resulting in the variation of UV-vis absorption and surface morphology. Proper addition of CH3NH3I not only enhances the absorption but also improves the efficiency of CH3NH3PbI3 solar cells from 11.13% to 13.37%. Photoluminescence spectra suggest that the improvement of device performance is attributed to the decrease of recombination rate of carriers in CH3NH3PbI3 absorber. This current method provides a highly repeatable route for enhancing the efficiency of CH3NH3PbI3 solar cell in the sequential solution deposition method.

A comparative DFT study of interactions of Au and small gold clusters Aun (n = 2-4) with CH3S and CH2 radicals

NASA Astrophysics Data System (ADS)

Blaško, Martin; Rajský, Tomáš; Urban, Miroslav

2017-03-01

We compare DFT binding energies (BEs) of Au and small gold clusters interacting with CH3S and CH2 ligands (Aun-L complexes, n = 1-4). The spin state and the binding mechanism in Aun-L varies with the participation of singly occupied non-bonding orbitals or doubly occupied lone-pair orbitals of a ligand and on the number of atoms (even or odd) of Aun. The highest BE, 354 kJ/mol, exhibits the Au3-CH2 complex with the covalent bond in which participate two singly occupied orbitals of the triplet state of CH2. With CH3S the highest BE (277 kJ/mol) is calculated for Au3-SCH3 with the single Au-S bond.

Relativistic GW calculations on CH3NH3PbI3 and CH3NH3SnI3 perovskites for solar cell applications.

PubMed

Umari, Paolo; Mosconi, Edoardo; De Angelis, Filippo

2014-03-26

Hybrid AMX3 perovskites (A = Cs, CH3NH3; M = Sn, Pb; X = halide) have revolutionized the scenario of emerging photovoltaic technologies, with very recent results demonstrating 15% efficient solar cells. The CH3NH3PbI3/MAPb(I(1-x)Cl(x))3 perovskites have dominated the field, while the similar CH3NH3SnI3 has not been exploited for photovoltaic applications. Replacement of Pb by Sn would facilitate the large uptake of perovskite-based photovoltaics. Despite the extremely fast progress, the materials electronic properties which are key to the photovoltaic performance are relatively little understood. Density Functional Theory electronic structure methods have so far delivered an unbalanced description of Pb- and Sn-based perovskites. Here we develop an effective GW method incorporating spin-orbit coupling which allows us to accurately model the electronic, optical and transport properties of CH3NH3SnI3 and CH3NH3PbI3, opening the way to new materials design. The different CH3NH3SnI3 and CH3NH3PbI3 electronic properties are discussed in light of their exploitation for solar cells, and found to be dominantly due to relativistic effects. These effects stabilize the CH3NH3PbI3 material towards oxidation, by inducing a deeper valence band edge. Relativistic effects, however, also increase the material band-gap compared to CH3NH3SnI3, due to the valence band energy downshift (~0.7 eV) being only partly compensated by the conduction band downshift (~0.2 eV).

Relativistic GW calculations on CH3NH3PbI3 and CH3NH3SnI3 Perovskites for Solar Cell Applications

PubMed Central

Umari, Paolo; Mosconi, Edoardo; De Angelis, Filippo

2014-01-01

Hybrid AMX3 perovskites (A = Cs, CH3NH3; M = Sn, Pb; X = halide) have revolutionized the scenario of emerging photovoltaic technologies, with very recent results demonstrating 15% efficient solar cells. The CH3NH3PbI3/MAPb(I1−xClx)3 perovskites have dominated the field, while the similar CH3NH3SnI3 has not been exploited for photovoltaic applications. Replacement of Pb by Sn would facilitate the large uptake of perovskite-based photovoltaics. Despite the extremely fast progress, the materials electronic properties which are key to the photovoltaic performance are relatively little understood. Density Functional Theory electronic structure methods have so far delivered an unbalanced description of Pb- and Sn-based perovskites. Here we develop an effective GW method incorporating spin-orbit coupling which allows us to accurately model the electronic, optical and transport properties of CH3NH3SnI3 and CH3NH3PbI3, opening the way to new materials design. The different CH3NH3SnI3 and CH3NH3PbI3 electronic properties are discussed in light of their exploitation for solar cells, and found to be dominantly due to relativistic effects. These effects stabilize the CH3NH3PbI3 material towards oxidation, by inducing a deeper valence band edge. Relativistic effects, however, also increase the material band-gap compared to CH3NH3SnI3, due to the valence band energy downshift (~0.7 eV) being only partly compensated by the conduction band downshift (~0.2 eV). PMID:24667758

Exploring the Reactivity Trends in the E2 and SN2 Reactions of X(-) + CH3CH2Cl (X = F, Cl, Br, HO, HS, HSe, NH2 PH2, AsH2, CH3, SiH3, and GeH3).

PubMed

Wu, Xiao-Peng; Sun, Xiao-Ming; Wei, Xi-Guang; Ren, Yi; Wong, Ning-Bew; Li, Wai-Kee

2009-06-09

The reactivity order of 12 anions toward ethyl chloride has been investigated by using the G2(+) method, and the competitive E2 and SN2 reactions are discussed and compared. The reactions studied are X(-) + CH3CH2Cl → HX + CH2═CH2 + Cl(-) and X(-) + CH3CH2Cl → CH3CH2X + Cl(-), with X = F, Cl, Br, HO, HS, HSe, NH2 PH2, AsH2, CH3, SiH3, and GeH3. Our results indicate that there is no general and straightforward relationship between the overall barriers and the proton affinity (PA) of X(-); instead, discernible linear correlations only exist for the X's within the same group of the periodic table. Similar correlations are also found with the electronegativity of central atoms in X, deformation energy of the E2 transition state (TS), and the overall enthalpy of reaction. It is revealed that the electronegativity will significantly affect the barrier height, and a more electronegative X will stabilize the E2 and SN2 transition states. Multiple linear regression analysis shows that there is a reasonable linear correlation between E2 (or SN2) overall barriers and the linear combination of PA of X(-) and electronegativity of the central atom.

Treatment with Ruta graveolens 5CH and Rhus toxicodendron 9CH may reduce joint pain and stiffness linked to aromatase inhibitors in women with early breast cancer: results of a pilot observational study.

PubMed

Karp, Jean-Claude; Sanchez, Carole; Guilbert, Philippe; Mina, William; Demonceaux, Antoine; Curé, Hervé

2016-11-01

To determine the possible effect of two homeopathic medicines, Ruta graveolens 5CH and Rhus toxicodendron 9CH, in the prevention of aromatase inhibitor (AI) associated joint pain and/or stiffness in women with early, hormone-receptor positive, breast cancer. This prospective, unrandomized observational study was carried out between April and October 2014. Women were recruited in two groups, according to which of the two study centres they attended: one receiving homeopathy in addition to standard treatment (group H) and a control group, receiving standard treatment (group C). All women were treated with an AI. In addition, women in group H also took Ruta graveolens 5CH and Rhus toxicodendron 9CH (5 granules, twice a day) up to 7 days before starting AI treatment. The homeopathic medicines were continued for 3 months. Demographic and clinical data were recorded using a self-assessment questionnaire at inclusion (T0) and 3 months (T3). Primary evaluation criteria were the evolution of scores for joint pain and stiffness, the impact of pain on sleep and analgesic consumption in the two groups after 3 months of treatment. Forty patients (mean age 64.9±8.1 years) were recruited, 20 in each group. Two-thirds of the patients had joint pain before starting AI treatment. There was a significant difference in the evolution of mean composite pain score between T0 and T3 in the two groups (-1.3 in group H vs. +3.4 in group C; p=0.0001). The individual components of the pain score (frequency, intensity and number of sites of pain) also decreased significantly in group H. Nine patients in group C (45%) vs. 1 (5%) in group H increased their analgesic consumption between T0 and T3 (p=0.0076). After 3 months of treatment, joint pain had a worse impact on sleep in patients in group C (35% vs. 0% of patients; p=0.0083). The differences observed in the evolution of morning and daytime stiffness between the two groups were smaller (p=0.053 and p=0.33, respectively), with the exception

ChIP-seq: advantages and challenges of a maturing technology.

PubMed

Park, Peter J

2009-10-01

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a technique for genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes. Owing to the tremendous progress in next-generation sequencing technology, ChIP-seq offers higher resolution, less noise and greater coverage than its array-based predecessor ChIP-chip. With the decreasing cost of sequencing, ChIP-seq has become an indispensable tool for studying gene regulation and epigenetic mechanisms. In this Review, I describe the benefits and challenges in harnessing this technique with an emphasis on issues related to experimental design and data analysis. ChIP-seq experiments generate large quantities of data, and effective computational analysis will be crucial for uncovering biological mechanisms.

Emendation of genus Achromobacter and Achromobacter xylosoxidans (Yabuuchi and Yano) and proposal of Achromobacter ruhlandii (Packer and Vishniac) comb. nov., Achromobacter piechaudii (Kiredjian et al.) comb. nov., and Achromobacter xylosoxidans subsp. denitrificans (Rüger and Tan) comb. nov.

PubMed

Yabuuchi, E; Kawamura, Y; Kosako, Y; Ezaki, T

1998-01-01

Based on the results of GC content determination and 16S rRNA sequence analysis among the type strains of Achromobacter xylosoxidans, 4 Alcaligenes species, 5 Bordetella species, and 12 species of 4 other genera, the separation of genus Achromobacter Yabuuchi and Yano 1981, with the type species Achromobacter xylosoxidans, is confirmed. Alcaligenes ruhlandii (Packer and Vishniac) Aragno and Schlegel 1992 is a distinct species and not a senior synonym of Achromobacter xylosoxidans. Alcaligenes ruhlandii and Alcaligenes piechaudii Kiredjian et al 1986 are transferred to genus Achromobacter. Thus 2 new combinations, Achromobacter ruhlandii (Packer and Vishniac) and Achromobacter piechaudii (Kiredjian et al) are proposed; their type strains are ATCC 15749 and ATCC 43552, respectively. Alcaligenes denitrificans Rüger and Tan 1983 is also transferred to genus Achromobacter and ranked down to the subspecies of Achromobacter xylosoxidans. Thus a new subspecies name, Achromobacter xylosoxidans subsp. denitrificans (Rüger and Tan) is proposed. The type strain of the subspecies is ATCC 15173. This proposal automatically creates type subspecies, Achromobacter xylosoxidans subsp. xylosoxidans, with type strain ATCC 27061. An emended description of genus Achromobacter and of type species Achromobacter xylosoxidans are given.

Metabolism of Acrylate to β-Hydroxypropionate and Its Role in Dimethylsulfoniopropionate Lyase Induction by a Salt Marsh Sediment Bacterium, Alcaligenes faecalis M3A

PubMed Central

Ansede, John H.; Pellechia, Perry J.; Yoch, Duane C.

1999-01-01

Dimethylsulfoniopropionate (DMSP) is degraded to dimethylsulfide (DMS) and acrylate by the enzyme DMSP lyase. DMS or acrylate can serve as a carbon source for both free-living and endophytic bacteria in the marine environment. In this study, we report on the mechanism of DMSP-acrylate metabolism by Alcaligenes faecalis M3A. Suspensions of citrate-grown cells expressed a low level of DMSP lyase activity that could be induced to much higher levels in the presence of DMSP, acrylate, and its metabolic product, β-hydroxypropionate. DMSP was degraded outside the cell, resulting in an extracellular accumulation of acrylate, which in suspensions of citrate-grown cells was then metabolized at a low endogenous rate. The inducible nature of acrylate metabolism was evidenced by both an increase in the rate of its degradation over time and the ability of acrylate-grown cells to metabolize this molecule at about an eight times higher rate than citrate-grown cells. Therefore, acrylate induces both its production (from DMSP) and its degradation by an acrylase enzyme. 1H and 13C nuclear magnetic resonance analyses were used to identify the products resulting from [1-13C]acrylate metabolism. The results indicated that A. faecalis first metabolized acrylate to β-hydroxypropionate outside the cell, which was followed by its intracellular accumulation and subsequent induction of DMSP lyase activity. In summary, the mechanism of DMSP degradation to acrylate and the subsequent degradation of acrylate to β-hydroxypropionate in the aerobic β-Proteobacterium A. faecalis has been described. PMID:10543825

ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data.

PubMed

Zhou, Ke-Ren; Liu, Shun; Sun, Wen-Ju; Zheng, Ling-Ling; Zhou, Hui; Yang, Jian-Hua; Qu, Liang-Hu

2017-01-04

The abnormal transcriptional regulation of non-coding RNAs (ncRNAs) and protein-coding genes (PCGs) is contributed to various biological processes and linked with human diseases, but the underlying mechanisms remain elusive. In this study, we developed ChIPBase v2.0 (http://rna.sysu.edu.cn/chipbase/) to explore the transcriptional regulatory networks of ncRNAs and PCGs. ChIPBase v2.0 has been expanded with ∼10 200 curated ChIP-seq datasets, which represent about 20 times expansion when comparing to the previous released version. We identified thousands of binding motif matrices and their binding sites from ChIP-seq data of DNA-binding proteins and predicted millions of transcriptional regulatory relationships between transcription factors (TFs) and genes. We constructed 'Regulator' module to predict hundreds of TFs and histone modifications that were involved in or affected transcription of ncRNAs and PCGs. Moreover, we built a web-based tool, Co-Expression, to explore the co-expression patterns between DNA-binding proteins and various types of genes by integrating the gene expression profiles of ∼10 000 tumor samples and ∼9100 normal tissues and cell lines. ChIPBase also provides a ChIP-Function tool and a genome browser to predict functions of diverse genes and visualize various ChIP-seq data. This study will greatly expand our understanding of the transcriptional regulations of ncRNAs and PCGs. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Contribution of Anthropogenic and Natural Emissions to Global CH4 Balances by Utilizing δ13C-CH4 Observations in CarbonTracker Data Assimilation System (CTDAS)

NASA Astrophysics Data System (ADS)

Kangasaho, V. E.; Tsuruta, A.; Aalto, T.; Backman, L. B.; Houweling, S.; Krol, M. C.; Peters, W.; van der Laan-Luijkx, I. T.; Lienert, S.; Joos, F.; Dlugokencky, E. J.; Michael, S.; White, J. W. C.

2017-12-01

The atmospheric burden of CH4 has more than doubled since preindustrial time. Evaluating the contribution from anthropogenic and natural emissions to the global methane budget is of great importance to better understand the significance of different sources at the global scale, and their contribution to changes in growth rate of atmospheric CH4 before and after 2006. In addition, observations of δ13C-CH4 suggest an increase in natural sources after 2006, which matches the observed increase and variation of CH4 abudance. Methane emission sources can be identified using δ13C-CH4, because different sources produce methane with process-specific isotopic signatures. This study focuses on inversion model based estimates of global anthropogenic and natural methane emission rates to evaluate the existing methane emission estimates with a new δ13C-CH4 inversion system. In situ measurements of atmospheric methane and δ13C-CH4 isotopic signature, provided by the NOAA Global Monitoring Division and the Institute of Arctic and Alpine Research, will be assimilated into the CTDAS-13C-CH4. The system uses the TM5 atmospheric transport model as an observation operator, constrained by ECMWF ERA Interim meteorological fields, and off-line TM5 chemistry fields to account for the atmospheric methane sink. LPX-Bern DYPTOP ecosystem model is used for prior natural methane emissions from wetlands, peatlands and mineral soils, GFED v4 for prior fire emissions and EDGAR v4.2 FT2010 inventory for prior anthropogenic emissions. The EDGAR antropogenic emissions are re-divided into enteric fermentation and manure management, landfills and waste water, rice, coal, oil and gas, and residential emissions, and the trend of total emissions is scaled to match optimized anthropogenic emissions from CTE-CH4. In addition to these categories, emissions from termites and oceans are included. Process specific δ13C-CH4 isotopic signatures are assigned to each emission source to estimate 13CH4 fraction

The Grammar of Ch'orti' Maya Folktales

ERIC Educational Resources Information Center

Dugan, James Timothy

2014-01-01

This study describes the grammar of the Ch'orti' Maya language as it appears in a collection of oral literature. I collected the stories that form the basis of this study in and around Jocotan, Guatemala, during 2004 and 2005. I worked with bilingual story-tellers to make audio recordings of the original Ch'orti'-language tales, produce textual…

How Many Ch-Class NEOs Do We Expect?

NASA Astrophysics Data System (ADS)

Rivkin, A. S.; DeMeo, F. E.

2017-09-01

The Ch spectral class is thought to contain objects that have water in their minerals, and they are of great interest to scientists and the nascent asteroid mining industry. We use models of asteroid delivery to near-Earth space and measurements of the different compositions of asteroids to estimate there should be at least 20 Ch asteroids larger than 100 m that are more accessible than the Moon, though we note that there are some untested assumptions that lead to that number. Further work must be done to identify the specific Ch asteroids.

Characterization of the Minimum Energy Paths for the Reactions of CH(X(sup 2 Pi) and (1)CH2 with C2H2

NASA Technical Reports Server (NTRS)

Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

1994-01-01

The reactions of CH(sup 2 Pi) and singlet methylene (1)CH2 with acetylene lead to intermediates which may be important in soot formation. CH(sup 2 Pi) + acetylene leads to CHCHCH (C3H3), CHCCH (C3H2), and propargyl (CH2CCH). (1)CH2 + acetylene leads to cyclopropene and propargyl. All of these reaction products are formed with no barrier. Miller and Melius have previously discussed the dimerization of propargyl to give benzene. C3H3 and C3H2 can dimerize with no barrier to give benzene and para-benzyne, respectively. C3H3 and C3H2 can also add to smaller polynuclear aromatic hydrocarbons (PAH), and may be important species in forming larger PAH or fullerenes.

34 CFR 34.14 - Burden of proof.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 34 Education 1 2010-07-01 2010-07-01 false Burden of proof. 34.14 Section 34.14 Education Office of the Secretary, Department of Education ADMINISTRATIVE WAGE GARNISHMENT § 34.14 Burden of proof. (a... those in § 34.24. (d)(1) If you object on the ground that applicable law bars us from collecting the...

New derivatives of 3,4-dihydroisoquinoline-3-carboxylic acid with free-radical scavenging, D-amino acid oxidase, acetylcholinesterase and butyrylcholinesterase inhibitory activity.

PubMed

Solecka, Jolanta; Guśpiel, Adam; Postek, Magdalena; Ziemska, Joanna; Kawęcki, Robert; Lęczycka, Katarzyna; Osior, Agnieszka; Pietrzak, Bartłomiej; Pypowski, Krzysztof; Wyrzykowska, Agata

2014-09-30

A series of 3,4-dihydroisoquinoline-3-carboxylic acid derivatives were synthesised and tested for their free-radical scavenging activity using 2,2-diphenyl-1-picrylhydrazyl radical (DPPH·), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical (ABTS·+), superoxide anion radical (O2·-) and nitric oxide radical (·NO) assays. We also studied d-amino acid oxidase (DAAO), acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibitory activity. Almost each of newly synthesised compounds exhibited radical scavenging capabilities. Moreover, several compounds showed moderate inhibitory activities against DAAO, AChE and BuChE. Compounds with significant free-radical scavenging activity may be potential candidates for therapeutics used in oxidative-stress-related diseases.

Sources and sinks of methane in the African Savanna. CH4 emissions from biomass burning

NASA Astrophysics Data System (ADS)

Delmas, R. A.; Marenco, A.; Tathy, J. P.; Cros, B.; Baudet, J. G. R.

1991-04-01

Sources and sinks of atmospheric methane are studied in savanna regions of west and central Africa. Flux measured over dry savanna soils, using static chambers, is always negative the average uptake rate being 2×1010 molecules/cm2/s. In these regions, sources are linked to biomass burning. Methane and CO2 emission from combustion of savanna plants and wood is studied by both field experiments and laboratory experiments using a combustion chamber. For savanna plants most of the carbon (85%) contained in the biomaterial is volatilized as CO2 and 0.1 to 0.25% as methane. For graminaceous plants like loudetia simplex the ratio C-CH4/C-CO2 is 0.11%; it is 0.28% for hyparrhenia the other main type of savanna plants and it attains 1.4% for the combustion of wood. In natural fire plumes this ratio is around 0.26% for savanna fires and 0.56 to 2.22% for forest fires. These results show that methane release is highly dependent on the type of combustion. Methane to CO2 ratios are also studied in vertical profiles in the troposphere taken during the TROPOZ I campaign, an aerial research expedition carried out over west Africa during the bushfire period. Within polluted layers, the average ratio of CH4 to CO2 excess over ambient air concentration is 0.34%. These results show that biomass burning in tropical Africa constitutes an important source of atmospheric methane estimated to about 9.2×106 T(CH4)/yr.

Microwave Spectroscopic Investigations of the C-H\\cdotsπ Containing Complexes CH_2F_2\\cdotsPROPYNE and CH_2ClF\\cdotsPROPYNE

NASA Astrophysics Data System (ADS)

Peebles, Rebecca A.; Peebles, Sean A.; Christenholz, Cori L.; Ernst, Anthony A.; Dhahir, Yasser J.

2013-06-01

The spectra of the CH_2F_2\\cdotspropyne and CH_2ClF\\cdotspropyne complexes have been studied by chirped-pulse and resonant cavity Fourier-transform microwave spectroscopy and by ab initio calculations at the MP2/6-311++G(2d,2p) level. Both complexes contain C-H\\cdotsπ contacts, with the halogen atoms angled towards the methyl group end of the propyne. While CH_2F_2\\cdotspropyne has C_s symmetry, CH_2ClF\\cdotspropyne has C_1 symmetry, with the fluorine and chlorine atoms straddling the propyne. Investigation of four single ^{13}C and the DC≡CCH_3 isotopologues in CH_2F_2\\cdotspropyne has allowed a detailed structural determination, while only the ^{35}Cl and ^{37}Cl isotopologues have so far been assigned for CH_2ClF\\cdotspropyne. Experimental data will be compared with ab initio results and with the analogous acetylene complexes, both of which have C_s symmetry structures, with double C-H\\cdotsπ interactions.

(Phosphinoalkyl)silanes. 4.(1) Hydrozirconation as a Non-Photochemical Route to (Phosphinopropyl)silanes: Facile Assembly of the Bis(3-(diphenylphosphino)propyl)silyl ("biPSi") Ligand Framework. Access to the Related Poly(3-(dimethylsilyl)propyl)phosphines R(n)()P(CH(2)CH(2)CH(2)SiMe(2)H)(3)(-)(n)() (n = 1, R = Ph; n = 0).

PubMed

Zhou, Xiaobing; Stobart, Stephen R.; Gossage, Robert A.

1997-08-13

Treatment of SiEt(3)(CH=CH(2)) with ZrCp(2)HCl (Schwartz's reagent) followed by reaction with PPh(2)Cl provides a high-yield (75%) route to Ph(2)PCH(2)CH(2)SiEt(3), and accordingly hydrozirconation of CH(2)=CHCH(2)SiHMe(2) affords the intermediate ZrCp(2)(CH(2)CH(2)CH(2)SiHMe(2))Cl (2). The latter, which is very sensitive to hydrolysis and reacts with HCl forming SiHMe(2)Pr(n)() and with NBS or I(2) affording SiHMe(2)CH(2)CH(2)CH(2)X (X = Br (3), I (4)), behaves similarly with PPh(2)Cl, PPhCl(2), or PBr(3) undergoing cleavage to the known Ph(2)PCH(2)CH(2)CH(2)SiMe(2)H (i.e. chelH, A) and the novel bis- and tris(silylpropyl)phosphines PhP(CH(2)CH(2)CH(2)SiMe(2)H)(2) (5) and P(CH(2)CH(2)CH(2)SiMe(2)H)(3) (6), respectively, with concomitant formation of ZrCp(2)Cl(2). Corresponding hydroboration of allylsilanes is facile, but subsequent phosphine halide cleavage yields (phosphinoalkyl)silanes only as constituents of intractable mixtures. Hydrozirconation followed by phosphination with PPh(2)Cl also converts SiHMe(CH(2)CH=CH(2))(2) to SiHMe(CH(2)CH(2)CH(2)PPh(2))(2) (i.e. biPSiH, B) together with a propyl analogue Ph(2)PCH(2)CH(2)CH(2)SiMe(Pr(n)())H (7) of A (ca. 2:1 ratio), as well as SiH(CH(2)CH=CH(2))(3) to a mixture (ca. 5:2:1 ratio) of SiH(CH(2)CH(2)CH(2)PPh(2))(3) (i.e. triPSiH, C), a new analogue SiH(Pr(n)())(CH(2)CH(2)CH(2)PPh(2))(2) (8) of B, and a further analogue Ph(2)PCH(2)CH(2)CH(2)SiHPr(n)()(2) (9) of A. A further analogue SiH(2)(CH(2)CH(2)CH(2)PPh(2))(2) (10) of biPSiH (B) is obtained similarly starting from SiH(2)(CH(2)CH=CH(2))(2). Steric control of silylalkyl cleavage from 2 is indicated by the fact that, like PPh(2)Cl (which forms B), two further biPSiH analogues SiH(Me)[CH(2)CH(2)CH(2)P(n-hex)(2)](2) (11) and SiH(Me)(CH(2)CH(2)CH(2)PPhBz)(2) (12) were obtained using P(n-hex)(2)Cl (i.e. n-hex = CH(3)(CH(2))(4)CH(2)-) or PPhBzCl (i.e. Bz = -CH(2)C(6)H(5)), respectively, whereas neither PPr(i)(2)Cl nor PBu(t)(2)Cl led to (phosphinoalkyl)silane formation

40 CFR 1065.660 - THC, NMHC, and CH4 determination.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 33 2014-07-01 2014-07-01 false THC, NMHC, and CH4 determination. 1065... POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calculations and Data Requirements § 1065.660 THC, NMHC, and CH4 determination. (a) THC determination and initial THC/CH 4 contamination corrections. (1) If we...

40 CFR 1065.660 - THC, NMHC, and CH4 determination.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 33 2011-07-01 2011-07-01 false THC, NMHC, and CH4 determination. 1065... POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calculations and Data Requirements § 1065.660 THC, NMHC, and CH4 determination. (a) THC determination and THC/CH 4 initial contamination corrections. (1) If we...

Gas-Phase Synthesis and Characterization of CH4-Loaded Hydroquinone Clathrates

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

Lee, J.; Lee, Y; Takeya, S

2010-01-01

A CH{sub 4}-loaded hydroquinone (HQ) clathrate was synthesized via a gas-phase reaction using the {alpha}-form of crystalline HQ and CH{sub 4} gas at 12 MPa and room temperature. Solid-state {sup 13}C cross-polarization/magic angle spinning (CP/MAS) NMR and Raman spectroscopic measurements confirm the incorporation of CH{sub 4} molecules into the cages of the HQ clathrate framework. The chemical analysis indicates that about 69% of the cages are filled by CH{sub 4} molecules, that is, 0.69 CH{sub 4} per three HQ molecules. Rietveld refinement using synchrotron X-ray powder diffraction (XRD) data shows that the CH{sub 4}-loaded HQ clathrate adopts the {beta}-form ofmore » HQ clathrate in a hexagonal space group R3 with lattice parameters of a = 16.6191 {angstrom} and c = 5.5038 {angstrom}. Time-resolved synchrotron XRD and quadrupole mass spectroscopic measurements show that the CH{sub 4}-loaded HQ clathrate is stable up to 368 K and gradually transforms to the {alpha}-form by releasing the confined CH{sub 4} gases between 368-378 K. Using solid-state {sup 13}C CP/MAS NMR, the reaction kinetics between the {alpha}-form HQ and CH{sub 4} gas is qualitatively described in terms of the particle size of the crystalline HQ.« less

Arctic tundra and mountain landscapes are persistent sinks of atmospheric CH4

NASA Astrophysics Data System (ADS)

Christiansen, Jesper; Winkler, Renato; Juncher Jørgensen, Christian

2017-04-01

Recent studies have shown significant rates of net uptake of atmospheric methane (CH4) in Arctic tundra soils. Oxidation of CH4 in these cold, dry soils in the Arctic region can counteract CH4 emissions from wetlands and play a potential important role for the net Arctic CH4 budget. However, significant knowledge gaps exist on the overall magnitude of the net CH4 sink in these cold, dry systems as the spatial and environmental limits for CH4 oxidation has not been determined. In particular, the extent, magnitude and drivers of CH4 oxidation in mountains and alpine landforms, which occupy large land areas in the Arctic and High Arctic has not yet been investigated leaving a potential vast CH4 sink unquantified with major potential implications for our conceptual view of Arctic CH4 budget in a changing climate. Here we present the results from two expeditions in the summers of 2015 and 2016 from Disko Bay and in the pro-glacial landscape in vicinity of the Russell Glacier, Kangerlussuaq, Greenland, respectively. The aim of our work is to determine the magnitude and extent of net uptake of atmospheric CH4 across a variety of previously unexplored dry tundra and post-glacial landforms in the Arctic, i.e. marginal moraines and other glacial features at the Greenland ice sheet as well as mountain tops and outwash plains. We used high-precision, mobile cavity-ring-down spectrometers (e.g. model G4301 GasScouter, Picarro Inc.) to achieve reliable flux estimates in sub-ambient CH4 concentration levels with a 4-minute enclosure time per chamber measurement. Our results show a persistent net uptake of CH4 uptake in these dry, extreme environments that rival the sink strength observed in temperate forest soils, otherwise considered the primary global terrestrial sink of atmospheric CH4. In this dynamic glacial landscape the magnitude of the net CH4 uptake is mainly constrained by recent landscape evolution along glacier margins and meltwater systems. Utilizing the high

Coupled-cluster sum-frequency generation nonlinear susceptibilities of methyl (CH3) and methylene (CH2) groups.

PubMed

Tetsassi Feugmo, Conrard Giresse; Liégeois, Vincent; Champagne, Benoît

2017-11-15

The first vibrational sum frequency generation (SFG) spectra based on molecular properties calculated at the coupled cluster singles and doubles (CCSD) level of approximation have been simulated for interfacial model alkyl chains, providing benchmark data for comparisons with approximate methods, including density functional theory (DFT). The approach proceeds in three steps. In the first two steps, the molecular spectral properties are determined: the vibrational normal modes and frequencies and then the derivatives of the dipole moment and of the polarizability with respect to the normal coordinates. These derivatives are evaluated with a numerical differentiation approach, of which the accuracy was monitored using Romberg's procedure. Then, in the last step, a three-layer model is employed to evaluate the macroscopic second-order nonlinear optical responses and thereby the simulated SFG spectra of the alkyl interface. Results emphasize the following facts: (i) the dipole and polarizability derivatives calculated at the DFT level with the B3LYP exchange-correlation functional can differ, with respect to CCSD, by as much as ±10 to 20% and ±20 to 50% for the CH 3 and CH 2 vibrations, respectively; (ii) these differences are enhanced when considering the SFG intensities as well as their variations as a function of the experimental configuration (ppp versus ssp) and as a function of the tilt and rotation angles, defining the orientation of the alkyl chain at the interface; (iii) these differences originate from both the vibrational normal coordinates and the Cartesian derivatives of the dipole moment and polarizability; (iv) freezing the successive fragments of the alkyl chain strongly modifies the SFG spectrum and enables highlighting the delocalization effects between the terminal CH 3 group and its neighboring CH 2 units; and finally (v) going from the free chain to the free methyl model, and further to C 3v constraints on leads to large variations of two ratios

Photochemical Modeling of CH3 Abundances in the Outer Solar System

NASA Technical Reports Server (NTRS)

Lee, Anthony Y. T.; Yung, Yuk L.; Moses, Julianne

2000-01-01

Recent measurements of methyl radicals (CH3) in the upper atmospheres of Saturn and Neptune by the Infrared Space Observatory (ISO) provide new constraints to photochemical models of hydrocarbon chemistry in the outer solar system. The derived column abundances of CH3 on Saturn above 10 mbar and Neptune above the 0.2 mbar pressure level are (2.5 - 6.0) x 10(exp 13) / sq cm and (0.7 - 2.8) x 10(exp 13) / sq cm, respectively. We use the updated Caltech/Jet Propulsion Laboratory photochemical model, which incorporates hydrocarbon photochemistry, vertical molecular and bulk atmospheric eddy diffusion, and realistic radiative transfer modeling, to study the CH3 abundances in the upper atmosphere of the giant planets and Titan. We identify the key reactions that control the concentrations of CH3 in the model, such as the three-body recombination reaction, CH3 + CH3 + M yields C2H6 + M. We evaluate and extrapolate the three-body rate constant of this reaction to the low-temperature limit (1.8 x 10(exp -16) T(sup -3.75) e(sup -300/T), T < 300 K) and compare methyl radical abundances in five atmospheres: Jupiter, Saturn, Uranus, Neptune, and Titan. The sensitivity of our models to the rate coefficients for the reactions H + CH3 + M yields CH4 + M, H + C2H3 yields C2H2 + H2, (sup 1)CH2 + H2 yields CH3 + H, and H + C2H5 yields 2CH3, the branching ratios of CH4 photolysis, vertical mixing in the five atmospheres, and Lyman alpha photon enhancement at the orbit of Neptune have all been tested. The results of our model CH3 abundances for both Saturn (5.1 x 10(exp 13) / sq cm) and Neptune (2.2 x 10(exp 13) / sq cm) show good agreement with ISO Short Wavelength Spectrometer measurements. Using the same chemical reaction set, our calculations also successfully generate vertical profiles of stable hydrocarbons consistent with Voyager and ground-based measurements in these outer solar system atmospheres. Predictions of CH3 column concentrations (for p <= 0.2 mbar) in the atmospheres

Megafauna and frozen soil: the drivers of atmospheric CH4 dynamics

NASA Astrophysics Data System (ADS)

Zimov, N.; Zimov, S. A.

2010-12-01

During the last deglaciation (LD) a strong increase in atmospheric methane (CH4) concentrations occurred simultaneously with a rise in Greenland temperatures indicating that in the north, during this time period, strong CH4 sources “awakened”, as additionally documented by the appearance of a strong gradient between northern (Greenland) and southern (Antarctica) hemisphere atmospheric CH4 concentrations. This rise could not be caused by wetland expansion. A reconstruction of peatland formation dynamics has indicated that wetlands on Earth were few in LD and only actively expanded 10,000 yr BP, after atmospheric CH4 concentrations began to decline. Destabilization of methane clathrates also could not be the source for atmospheric CH4 increase. Geological CH4 (including methane clathrates) has the highest deuterium content (δD) among all of the known sources of CH4 while atmospheric CH4 δD values determined for the LD were record low. To explain recorded atmospheric CH4 and its isotopic dynamics required a strong northern source, which was active only during the LD and that provided very low δD CH4 values. Such a source is permafrost thawing under anaerobic conditions (or better stated soils of mammoth steppe-tundra ecosystems). Permafrost thawing is the strongest, among known, wetland sources (usually over 100g CH4/m2yr) and has a unique isotopic signature (δD = -400 per mil (-338 to -479 per mil), δ13C = -73 per mil (-58 to -99 per mil)). The main sources of atmospheric CH4 have different isotopic signatures (δ13C, δD). The isotopic content of atmospheric CH4 is a simple function of the weight average for all of the sources. Inclusion of permafrost source into a budget model of the atmospheric methane and its isotopes allowed us to reconstruct the dynamics of methane’s main sources. Model indicated geological source to be negligible as in LGM so and in LD and Holocene. During the glaciation, the largest methane source was megafauna, whose 1

Equilibrium Acidities and Homolytic Bond Dissociation Enthalpies of the Acidic C-H Bonds in P-(Para-substituted benzyl)triphenylphosphonium Cations and Related Cations.

PubMed

Zhang, Xian-Man; Fry, Albert J.; Bordwell, Frederick G.

1996-06-14

Equilibrium acidities (pK(HA)) of six P-(para-substituted benzyl)triphenylphosphonium (p-GC(6)H(4)CH(2)PPh(3)(+)) cations, P-allyltriphenylphosphonium cation, P-cinnamyltriphenylphosphonium cation, and As-(p-cyanobenzyl)triphenylarsonium cation, together with the oxidation potentials [E(ox)(A(-))] of their conjugate anions (ylides) have been measured in dimethyl sulfoxide (DMSO) solution. The acidifying effects of the alpha-triphenylphosphonium groups on the acidic C-H bonds in toluene and propene were found to be ca 25 pK(HA) units (34 kcal/mol). Introduction of an electron-withdrawing group such as 4-NO(2), 4-CN, or 4-Br into the para position of the benzyl ring in p-GC(6)H(4)CH(2)PPh(3)(+) cations resulted in an additional acidity increase, but introduction of the 4-OEt electron-donating group decreases the acidity. The equilibrium acidities of p-GC(6)H(4)CH(2)PPh(3)(+) cations were nicely linearly correlated with the Hammett sigma(-) constants of the substituents (G) with a slope of 4.78 pK(HA) units (R(2) = 0.992) (Figure 1). Reversible oxidation potentials of the P-(para-substituted benzyl)triphenylphosphonium ylides were obtained by fast scan cyclic voltammetry. The homolytic bond dissociation enthalpies (BDEs) of the acidic C-H bonds in these cations, estimated by combining their equilibrium acidities with the oxidation potentials of their corresponding conjugate anions, showed that the alpha-Ph(3)P(+) groups have negligible stabilizing or destabilizing effects on the adjacent radicals. The equilibrium acidity of As-(p-cyanobenzyl)triphenylarsonium cation is 4 pK(HA) units weaker than that of P-(p-cyanobenzyl)triphenylphosphonium cation, but the BDE of the acidic C-H bond in As-(p-cyanobenzyl)triphenylarsonium cation is ca 2 kcal/mol higher than that in P-(p-cyanobenzyl)triphenylphosphonium cation.

34 CFR 34.23 - Exclusions from garnishment.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 34 Education 1 2010-07-01 2010-07-01 false Exclusions from garnishment. 34.23 Section 34.23 Education Office of the Secretary, Department of Education ADMINISTRATIVE WAGE GARNISHMENT § 34.23... months. (b) You have the burden of informing us of the circumstances surrounding an involuntary...

Spectroscopic properties of morin in various CH3OH-H2O and CH3CN-H2O mixed solvents.

PubMed

Park, Hyoung-Ryun; Im, Seo-Eun; Seo, Jung-Ja; Kim, Bong-Gon; Yoon, Jin Ah; Bark, Ki-Min

2015-01-01

The specific fluorescence properties of morin (3,2',4',5,7-pentahydroxyflavone) were studied in various CH3OH-H2O and CH3CN-H2O mixed solvents. Although the dihedral angle is large in the S0 state, morin has an almost planar molecular structure in the S1 state owing to the very low rotational energy barrier around the interring bond between B and the A, C ring. The excited state intramolecular proton transfer (ESIPT) at the S1 state cannot occur immediately after excitation, S1 → S0 fluorescence can be observed. Two conformers, Morin A and B have been known. At the CH3OH-H2O, Morin B will be the principal species but at the CH3CN-H2O, Morin A is the principal species. At the CH3OH-H2O, owing to the large Franck-Condon (FC) factor for S2 → S1 internal convernal (IC) and flexible molecular structure, only S1 → S0 fluorescence was exhibited. At the CH3CN-H2O, as the FC factor for S2 → S1 IC is small and molecular structure is rigid, S2 → S0 and S1 → S0 dual fluorescence was observed. This abnormal fluorescence property was further supported by the small pK1 value, effective delocalization of the lone pair electrons of C(2')-OH to the A, C ring, and a theoretical calculation. © 2014 The American Society of Photobiology.

Le Châtelier reciprocal relations and the mechanical analog

NASA Astrophysics Data System (ADS)

Gilmore, Robert

1983-08-01

Le Châtelier's principle is discussed carefully in terms of two sets of simple thermodynamic examples. The principle is then formulated quantitatively for general thermodynamic systems. The formulation is in terms of a perturbation-response matrix, the Le Châtelier matrix [L]. Le Châtelier's principle is contained in the diagonal elements of this matrix, all of which exceed one. These matrix elements describe the response of a system to a perturbation of either its extensive or intensive variables. These response ratios are inverses of each other. The Le Châtelier matrix is symmetric, so that a new set of thermodynamic reciprocal relations is derived. This quantitative formulation is illustrated by a single simple example which includes the original examples and shows the reciprocities among them. The assumptions underlying this new quantitative formulation of Le Châtelier's principle are general and applicable to a wide variety of nonthermodynamic systems. Le Châtelier's principle is formulated quantitatively for mechanical systems in static equilibrium, and mechanical examples of this formulation are given.

A brief overview of the Chemistry-Aerosol Mediterranean Experiment (ChArMEx) database and campaign operation centre (ChOC)

NASA Astrophysics Data System (ADS)

Ferré, Hélène; Dulac, François; Belmahfoud, Nizar; Brissebrat, Guillaume; Cloché, Sophie; Descloitres, Jacques; Fleury, Laurence; Focsa, Loredana; Henriot, Nicolas; Ramage, Karim; Vermeulen, Anne

2016-04-01

Initiated in 2010 in the framework of the multidisciplinary research programme MISTRALS (Mediterranean Integrated Studies at Regional and Local Scales; http:www.mistrals-home.org), the Chemistry-Aerosol Mediterranean Experiment (ChArMEx, http://charmex.lsce.ipsl.fr/) aims at federating the scientific community for an updated assessment of the present and future state of the atmospheric environment in the Mediterranean Basin, and of its impacts on the regional climate, air quality, and marine biogeochemistry. The project combines mid- and long-term monitoring, intensive field campaigns, use of satellite data, and modelling studies. In this presentation we provide an overview of the campaign operation centre (http://choc.sedoo.fr/) and project database (http://mistrals.sedoo.fr/ChArMEx), at the end of the first experimental phase of the project that included a series of large campaigns based on airborne means (including balloons and various aircraft) and a network of surface stations. Those campaigns were performed mainly in the western Mediterranean basin in the summer of 2012, 2013 and 2014 with the help of the ChArMEx Operation Centre (ChOC), an open web site that has the objective to gather and display daily quick-looks from model forecasts and near-real time in situ and remote sensing observations of physical and chemical weather conditions relevant for the everyday campaign operation decisions. The ChOC is also useful for post campaign analyses and can be completed with a number of quick-looks of campaign results obtained later in order to offer an easy access to, and comprehensive view of all available data during the campaign period. The items included are selected according to the objectives and location of the given campaigns. The second experimental phase of ChArMEx from 2015 on is more focused on the eastern basin. In addition, the project operation centre is planned to be adapted for a joint MERMEX-ChArMEx oceanographic cruise (PEACETIME) for a study at

Ozone Depletion Potential of CH3Br

NASA Technical Reports Server (NTRS)

Sander, Stanley P.; Ko, Malcolm K. W.; Sze, Nien Dak; Scott, Courtney; Rodriquez, Jose M.; Weisenstein, Debra K.

1998-01-01

The ozone depletion potential (ODP) of methyl bromide (CH3Br) can be determined by combining the model-calculated bromine efficiency factor (BEF) for CH3Br and its atmospheric lifetime. This paper examines how changes in several key kinetic data affect BEF. The key reactions highlighted in this study include the reaction of BrO + H02, the absorption cross section of HOBr, the absorption cross section and the photolysis products of BrON02, and the heterogeneous conversion of BrON02 to HOBR and HN03 on aerosol particles. By combining the calculated BEF with the latest estimate of 0.7 year for the atmospheric lifetime of CH3Br, the likely value of ODP for CH3Br is 0.39. The model-calculated concentration of HBr (approximately 0.3 pptv) in the lower stratosphere is substantially smaller than the reported measured value of about I pptv. Recent publications suggested models can reproduce the measured value if one assumes a yield for HBr from the reaction of BrO + OH or from the reaction of BrO + H02. Although the DeAlore et al. evaluation concluded any substantial yield of HBr from BrO + HO2 is unlikely, for completeness, we calculate the effects of these assumed yields on BEF for CH3Br. Our calculations show that the effects are minimal: practically no impact for an assumed 1.3% yield of HBr from BrO + OH and 10% smaller for an assumed 0.6% yield from BrO + H02.

14 CFR 34.83-34.88 - [Reserved

Code of Federal Regulations, 2012 CFR

2012-01-01

... 14 Aeronautics and Space 1 2012-01-01 2012-01-01 false [Reserved] 34.83-34.88 Section 34.83-34.88 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF TRANSPORTATION AIRCRAFT FUEL VENTING AND EXHAUST EMISSION REQUIREMENTS FOR TURBINE ENGINE POWERED AIRPLANES Test Procedures for Engine Smoke...

Two-Photon Holographic Stimulation of ReaChR

PubMed Central

Chaigneau, Emmanuelle; Ronzitti, Emiliano; Gajowa, Marta A.; Soler-Llavina, Gilberto J.; Tanese, Dimitrii; Brureau, Anthony Y. B.; Papagiakoumou, Eirini; Zeng, Hongkui; Emiliani, Valentina

2016-01-01

Optogenetics provides a unique approach to remotely manipulate brain activity with light. Reaching the degree of spatiotemporal control necessary to dissect the role of individual cells in neuronal networks, some of which reside deep in the brain, requires joint progress in opsin engineering and light sculpting methods. Here we investigate for the first time two-photon stimulation of the red-shifted opsin ReaChR. We use two-photon (2P) holographic illumination to control the activation of individually chosen neurons expressing ReaChR in acute brain slices. We demonstrated reliable action potential generation in ReaChR-expressing neurons and studied holographic 2P-evoked spiking performances depending on illumination power and pulse width using an amplified laser and a standard femtosecond Ti:Sapphire oscillator laser. These findings provide detailed knowledge of ReaChR's behavior under 2P illumination paving the way for achieving in depth remote control of multiple cells with high spatiotemporal resolution deep within scattering tissue. PMID:27803649

Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments

PubMed Central

Welch, Rene; Chung, Dongjun; Grass, Jeffrey; Landick, Robert

2017-01-01

Abstract ChIP-exo/nexus experiments rely on innovative modifications of the commonly used ChIP-seq protocol for high resolution mapping of transcription factor binding sites. Although many aspects of the ChIP-exo data analysis are similar to those of ChIP-seq, these high throughput experiments pose a number of unique quality control and analysis challenges. We develop a novel statistical quality control pipeline and accompanying R/Bioconductor package, ChIPexoQual, to enable exploration and analysis of ChIP-exo and related experiments. ChIPexoQual evaluates a number of key issues including strand imbalance, library complexity, and signal enrichment of data. Assessment of these features are facilitated through diagnostic plots and summary statistics computed over regions of the genome with varying levels of coverage. We evaluated our QC pipeline with both large collections of public ChIP-exo/nexus data and multiple, new ChIP-exo datasets from Escherichia coli. ChIPexoQual analysis of these datasets resulted in guidelines for using these QC metrics across a wide range of sequencing depths and provided further insights for modelling ChIP-exo data. PMID:28911122

Kinetics of the Br2-CH3CHO Photochemical Chain Reaction

NASA Technical Reports Server (NTRS)

Nicovich, J. M.; Shackelford, C. J.; Wine, P. H.

1997-01-01

Time-resolved resonance fluorescence spectroscopy was employed in conjunction with laser flash photolysis of Br2 to study the kinetics of the two elementary steps in the photochemical chain reaction nBr2 + nCH3CHO + hv yields nCH3CBrO + nHBr. In the temperature range 255-400 K, the rate coefficient for the reaction Br((sup 2)P(sub 3/2)) + CH3CHO yields CH3CO + HBr is given by the Arrhenius expression k(sub 6)(T) = (1.51 +/- 0.20) x 10(exp -11) exp(-(364 +/- 41)/T)cu cm/(molecule.s). At 298 K, the reaction CH3CO + Br2 yields CH3CBrO + Br proceeds at a near gas kinetic rate, k(sub 7)(298 K) = (1.08 +/- 0.38) x 10(exp -10)cu cm/(molecule.s).

Hyperfine excitation of CH in collisions with atomic and molecular hydrogen

NASA Astrophysics Data System (ADS)

Dagdigian, Paul J.

2018-04-01

We investigate here the excitation of methylidene (CH) induced by collisions with atomic and molecular hydrogen (H and H2). The hyperfine-resolved rate coefficients were obtained from close coupling nuclear-spin-free scattering calculations. The calculations are based upon recent, high-accuracy calculations of the CH(X2Π)-H(2S) and CH(X2Π)-H2 potential energy surfaces. Cross-sections and rate coefficients for collisions with atomic H, para-H2, and ortho-H2 were computed for all transitions between the 32 hyperfine levels for CH(X2Π) involving the n ≤ 4 rotational levels for temperatures between 10 and 300 K. These rate coefficients should significantly aid in the interpretation of astronomical observations of CH spectra. As a first application, the excitation of CH is simulated for conditions in typical molecular clouds.

34 CFR 34.17 - Content of decision.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 34 Education 1 2010-07-01 2010-07-01 false Content of decision. 34.17 Section 34.17 Education Office of the Secretary, Department of Education ADMINISTRATIVE WAGE GARNISHMENT § 34.17 Content of... findings, analysis, and conclusions regarding objections raised to the existence or amount of the debt; (3...

Communication: Photodissociation of CH3CHO at 308 nm: Observation of H-roaming, CH3-roaming, and transition state pathways together along the ground state surface

NASA Astrophysics Data System (ADS)

Li, Hou-Kuan; Tsai, Po-Yu; Hung, Kai-Chan; Kasai, Toshio; Lin, King-Chuen

2015-01-01

Following photodissociation of acetaldehyde (CH3CHO) at 308 nm, the CO(v = 1-4) fragment is acquired using time-resolved Fourier-transform infrared emission spectroscopy. The CO(v = 1) rotational distribution shows a bimodal feature; the low- and high-J components result from H-roaming around CH3CO core and CH3-roaming around CHO radical, respectively, in consistency with a recent assignment by Kable and co-workers (Lee et al., Chem. Sci. 5, 4633 (2014)). The H-roaming pathway disappears at the CO(v ≥ 2) states, because of insufficient available energy following bond-breaking of H + CH3CO. By analyzing the CH4 emission spectrum, we obtained a bimodal vibrational distribution; the low-energy component is ascribed to the transition state (TS) pathway, consistent with prediction by quasiclassical trajectory calculations, while the high-energy component results from H- and CH3-roamings. A branching fraction of H-roaming/CH3-roaming/TS contribution is evaluated to be (8% ± 3%)/(68% ± 10%)/(25% ± 5%), in which the TS pathway was observed for the first time. The three pathways proceed concomitantly along the electronic ground state surface.

Radical routes to interstellar glycolaldehyde. The possibility of stereoselectivity in gas-phase polymerization reactions involving CH(2)O and ˙CH(2)OH.

PubMed

Wang, Tianfang; Bowie, John H

2010-10-21

A previous report that the interstellar molecule glycolaldehyde (HOCH(2)CHO) can be made from hydroxymethylene (HOCH:) and formaldehyde has been revisited at the CCSD(T)/6-311++G(3df,2p)//MP2/6-311++G(3df,2p) level of theory. This reaction competes with the formation of acetic acid and methylformate, molecules which have also been detected in interstellar clouds. Other possible modes of formation of glycolaldehyde by radical/radical reactions have been shown to be viable theoretically as follows: HO˙+˙CH2CHO -->HOCH2CHO [ΔG(Γ)(298K)=-303kJ mol⁻¹] HOCH2˙+˙CHO-->HOCH2CHO (-259kJ mol⁻¹). The species in these two processes are known interstellar molecules. Key radicals ˙CH(2)CHO and ˙CH(2)OH in these sequences have been shown to be stable for the microsecond duration of neutralization/reionization experiments in the dual collision cells of a VG ZAB 2HF mass spectrometer. The polymerization reaction HOCH(2)CH˙OH + nCH(2)O → HOCH(2)[CH(OH)](n)˙CHOH (n = 1 to 3) has been studied theoretically and shown to be energetically feasible, as is the cyclization reaction of HOCH(2)[(CH(2)OH)(4)]˙CHOH (in the presence of one molecule of water at the reacting centre) to form glucose. The probability of such a reaction sequence is small even if polymerization were to occur in interstellar ice containing a significant concentration of CH(2)O. The large number of stereoisomers produced by such a reaction sequence makes the formation of a particular sugar, again for example glucose, an inefficient synthesis. The possibility of stereoselectivity occurring during the polymerization was investigated for two diastereoisomers of HOCH(2)[(CHOH)](2)˙CHOH. No significant difference was found in the transition state energies for addition of CH(2)O to these two diastereoisomers, but a barrier difference of 12 kJ mol(-1) was found for the H transfer reactions ˙OCH(2)[(CHOH)](2)CH(2)OH → HOCH(2)[(CHOH)(2)˙CHOH of the two diastereoisomers.

Energetics of the O-H bond and of intramolecular hydrogen bonding in HOC6H4C(O)Y (Y = H, CH3, CH2CH=CH2, C[triple bond]CH, CH2F, NH2, NHCH3, NO2, OH, OCH3, OCN, CN, F, Cl, SH, and SCH3) compounds.

PubMed

Bernardes, Carlos E S; Minas da Piedade, Manuel E

2008-10-09

The energetics of the phenolic O-H bond in a series of 2- and 4-HOC 6H 4C(O)Y (Y = H, CH3, CH 2CH=CH2, C[triple bond]CH, CH2F, NH2, NHCH 3, NO2, OH, OCH3, OCN, CN, F, Cl, SH, and SCH3) compounds and of the intramolecular O...H hydrogen bond in 2-HOC 6H 4C(O)Y, was investigated by using a combination of experimental and theoretical methods. The standard molar enthalpies of formation of 2-hydroxybenzaldehyde (2HBA), 4-hydroxybenzaldehyde (4HBA), 2'-hydroxyacetophenone (2HAP), 2-hydroxybenzamide (2HBM), and 4-hydroxybenzamide (4HBM), at 298.15 K, were determined by micro- or macrocombustion calorimetry. The corresponding enthalpies of vaporization or sublimation were also measured by Calvet drop-calorimetry and Knudsen effusion measurements. The combination of the obtained experimental data led to Delta f H m (o)(2HBA, g) = -238.3 +/- 2.5 kJ.mol (-1), DeltafHm(o)(4HBA, g) = -220.3 +/- 2.0 kJ.mol(-1), Delta f H m (o)(2HAP, g) = -291.8 +/- 2.1 kJ.mol(-1), DeltafHm(o)(2HBM, g) = -304.8 +/- 1.5 kJ.mol (-1), and DeltafHm(o) (4HBM, g) = -278.4 +/- 2.4 kJ.mol (-1). These values, were used to assess the predictions of the B3LYP/6-31G(d,p), B3LYP/6-311+G(d,p), B3LYP/aug-cc-pVDZ, B3P86/6-31G(d,p), B3P86/6-311+G(d,p), B3P86/aug-cc-pVDZ, and CBS-QB3 methods, for the enthalpies of a series of isodesmic gas phase reactions. In general, the CBS-QB3 method was able to reproduce the experimental enthalpies of reaction within their uncertainties. The B3LYP/6-311+G(d,p) method, with a slightly poorer accuracy than the CBS-QB3 approach, achieved the best performance of the tested DFT models. It was further used to analyze the trends of the intramolecular O...H hydrogen bond in 2-HOC 6H 4C(O)Y evaluated by the ortho-para method and to compare the energetics of the phenolic O-H bond in 2- and 4-HOC 6H 4C(O)Y compounds. It was concluded that the O-H bond "strength" is systematically larger for 2-hydroxybenzoyl than for the corresponding 4-hydroxybenzoyl isomers mainly due to the presence of

RKR Franck-Condon factors for blue and ultraviolet transitions of some molecules of astrophysical interest and some comments on the interstellar abundance of CH, CH+ and SiH+.

NASA Technical Reports Server (NTRS)

Liszt, H. S.; Hayden Smith, W.

1972-01-01

RKR Franck-Condon factors for thirteen of the blue and ultraviolet transitions of AlF, AlO, BH, BD, CH, CD, CH(+), SiO and SiH(+) have been calculated. The interstellar abundances of CH, CH(+) and SiH(+) are discussed with regard to recent laboratory measurements, our Franck-Condon factors, and observations of the sun and the interstellar medium.

34 CFR 101.34 - Service-how made.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 34 Education 1 2010-07-01 2010-07-01 false Service-how made. 101.34 Section 101.34 Education Regulations of the Offices of the Department of Education OFFICE FOR CIVIL RIGHTS, DEPARTMENT OF EDUCATION... Documents § 101.34 Service—how made. Service shall be made by personal delivery of one copy to each person...

CH functionalization of heteroaromatic compounds by transition metal catalysis

NASA Astrophysics Data System (ADS)

Tanba, Shunsuke; Fujiwara, Taiki; Monguchi, Daiki; Mori, Atsunori

2010-06-01

Transition metal-catalyzed CH functioanlization of thiazoles and thiophenes are carried out. The reaction of thiophene with aryl halide in the presence of a palladium catalyst underwent the CC bond forming reaction at the CH bond of thiophene. By employing the reaction head-to-tail-type oligothiophene is synthesized in a stepwise manner. When several azoles are treated with secondary amines and amides in the presence of a copper catalyst, oxidative CH-NH coupling took place to form the carbon-nitrogen bond.

Towards the new CH2018 climate scenarios for Switzerland

NASA Astrophysics Data System (ADS)

Fischer, Andreas; Schär, Christoph; Croci-Maspoli, Mischa; Knutti, Reto; Liniger, Mark; Strassmann, Kuno

2017-04-01

There is a growing demand for regional assessments of future climate change and its impacts on society and ecosystems to inform and facilitate appropriate adaptation strategies. The basis for such assessments are consistent and up-to-date climate change scenarios on the local to regional scale. In Switzerland, an important step has been accomplished by the release of the climate scenarios in 2011 ("CH2011"). Since then, new climate model simulations have become available and the scientific understanding has improved. It is hence desirable to update these national scenarios. The new CH2018 scenarios are developed in the framework of the recently founded National Center for Climate Services (NCCS), a network consisting of several federal offices and academic partners. The CH2018 scenarios will build primarily upon the latest Euro-CORDEX regional climate model simulations assuming different pathways of future greenhouse gas concentrations. Compared to CH2011, more emphasis will be put on changes in extremes and in putting the projected changes in the context of observed variability. Results of a recently conducted survey on end-user needs in Switzerland will guide the development process toward the CH2018 scenarios. It ensures that the scenarios are presented and communicated in a user-oriented format and find a wide applicability across different sectors in Switzerland. In the presentation we will show the full methodological setup to generate the CH2018 scenarios and how consistency across the methods and products is maximized. First results on mean changes and selected indices will be presented. In terms of dissemination, the results of the user survey show the necessity to address all different user types of climate scenarios, especially the non-experts. Compared to CH2011, this implies a stronger focus on consulting, condensing complex information and providing tutorials. In the presentation, we will outline our plans on dissemination in order to adequately

CH/π Interactions in Carbohydrate Recognition.

PubMed

Spiwok, Vojtěch

2017-06-23

Many carbohydrate-binding proteins contain aromatic amino acid residues in their binding sites. These residues interact with carbohydrates in a stacking geometry via CH/π interactions. These interactions can be found in carbohydrate-binding proteins, including lectins, enzymes and carbohydrate transporters. Besides this, many non-protein aromatic molecules (natural as well as artificial) can bind saccharides using these interactions. Recent computational and experimental studies have shown that carbohydrate-aromatic CH/π interactions are dispersion interactions, tuned by electrostatics and partially stabilized by a hydrophobic effect in solvated systems.

Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application.

PubMed

Zhong, Jian; Ye, Zhenqing; Lenz, Samuel W; Clark, Chad R; Bharucha, Adil; Farrugia, Gianrico; Robertson, Keith D; Zhang, Zhiguo; Ordog, Tamas; Lee, Jeong-Heon

2017-12-21

Chromatin immunoprecipitation-sequencing (ChIP-seq) is a widely used epigenetic approach for investigating genome-wide protein-DNA interactions in cells and tissues. The approach has been relatively well established but several key steps still require further improvement. As a part of the procedure, immnoprecipitated DNA must undergo purification and library preparation for subsequent high-throughput sequencing. Current ChIP protocols typically yield nanogram quantities of immunoprecipitated DNA mainly depending on the target of interest and starting chromatin input amount. However, little information exists on the performance of reagents used for the purification of such minute amounts of immunoprecipitated DNA in ChIP elution buffer and their effects on ChIP-seq data. Here, we compared DNA recovery, library preparation efficiency, and ChIP-seq results obtained with several commercial DNA purification reagents applied to 1 ng ChIP DNA and also investigated the impact of conditions under which ChIP DNA is stored. We compared DNA recovery of ten commercial DNA purification reagents and phenol/chloroform extraction from 1 to 50 ng of immunopreciptated DNA in ChIP elution buffer. The recovery yield was significantly different with 1 ng of DNA while similar in higher DNA amounts. We also observed that the low nanogram range of purified DNA is prone to loss during storage depending on the type of polypropylene tube used. The immunoprecipitated DNA equivalent to 1 ng of purified DNA was subject to DNA purification and library preparation to evaluate the performance of four better performing purification reagents in ChIP-seq applications. Quantification of library DNAs indicated the selected purification kits have a negligible impact on the efficiency of library preparation. The resulting ChIP-seq data were comparable with the dataset generated by ENCODE consortium and were highly correlated between the data from different purification reagents. This study provides

34 CFR 34.17 - Content of decision.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 34 Education 1 2011-07-01 2011-07-01 false Content of decision. 34.17 Section 34.17 Education Office of the Secretary, Department of Education ADMINISTRATIVE WAGE GARNISHMENT § 34.17 Content of decision. (a) The written decision is based on the evidence contained in the hearing record. The decision includes— (1) A description of the evidence...

Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments.

PubMed

Welch, Rene; Chung, Dongjun; Grass, Jeffrey; Landick, Robert; Keles, Sündüz

2017-09-06

ChIP-exo/nexus experiments rely on innovative modifications of the commonly used ChIP-seq protocol for high resolution mapping of transcription factor binding sites. Although many aspects of the ChIP-exo data analysis are similar to those of ChIP-seq, these high throughput experiments pose a number of unique quality control and analysis challenges. We develop a novel statistical quality control pipeline and accompanying R/Bioconductor package, ChIPexoQual, to enable exploration and analysis of ChIP-exo and related experiments. ChIPexoQual evaluates a number of key issues including strand imbalance, library complexity, and signal enrichment of data. Assessment of these features are facilitated through diagnostic plots and summary statistics computed over regions of the genome with varying levels of coverage. We evaluated our QC pipeline with both large collections of public ChIP-exo/nexus data and multiple, new ChIP-exo datasets from Escherichia coli. ChIPexoQual analysis of these datasets resulted in guidelines for using these QC metrics across a wide range of sequencing depths and provided further insights for modelling ChIP-exo data. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Direct Dynamics Simulation of Dissociation of the [CH3--I--OH]- Ion-Molecule Complex

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

Xie, Jing; McClellan, Miranda; Sun, Rui

Direct dynamics simulations were used to study dissociation of the [CH3--I--OH]- complex ion, which was observed in a previous study of the OH- + CH3I gas phase reaction (J. Phys. Chem. A 2013, 117, 7162). Restricted B97-1 simulations were performed to study dissociation at 65, 75 and 100 kcal/mol and the [CH3--I--OH]- ion dissociated exponentially, in accord with RRKM theory. For these energies the major dissociation products are CH3I + OH-, CH2I- + H2O, and CH3OH + I-. Unrestricted B97-1 and restricted and unrestricted CAM-B3LYP simulations were also performed at 100 kcal/mol to compare with the restricted B97-1 results. Themore » {CH3I + OH-}:{CH2I- + H2O}:{CH3OH + I-} product ratio is 0.72 : 0.15 : 0.13, 0.81 : 0.05 : 0.14, 0.71 : 0.19 : 0.10 , and 0.83 : 0.13 : 0.04 for the restricted B97-1, unrestricted B97-1, restricted CAM-B3LYP, and unrestricted CAM-B3LYP simulations, respectively. Other product channels found are CH2 + I- + H2O, CH2 + I-(H2O), CH4 + IO-, CH3 - + IOH, and CH3 + IOH-. The CH3 - + IOH singlet products are only given by the restricted B97-1 simulation and the lower energy CH3 + IOH- doublet products are only formed by the unrestricted B97-1 simulation. Also studied were the direct and indirect atomic-level mechanisms for forming CH3I + OH-, CH2I- + H2O, and CH3OH + I-. The majority of CH3I + OH- were formed through a direct mechanism. For both CH2I- + H2O and CH3OH + I-, the direct mechanism is overall more important than the indirect mechanisms, with the round-about like mechanism the most important indirect mechanism at high excitation energies. Mechanism comparisons between the B97-1 and CAM-B3LYP simulations showed that formation of the CH3OH---I- complex is favored for the B97-1 simulations, while formation of the HO----HCH2I complex is favored for the CAM-B3LYP simulations. The unrestricted simulations give a higher percentage of indirect mechanisms than the restricted simulations. The possible role of the self-interaction error in

Scalable and sustainable electrochemical allylic C-H oxidation

NASA Astrophysics Data System (ADS)

Horn, Evan J.; Rosen, Brandon R.; Chen, Yong; Tang, Jiaze; Chen, Ke; Eastgate, Martin D.; Baran, Phil S.

2016-05-01

New methods and strategies for the direct functionalization of C-H bonds are beginning to reshape the field of retrosynthetic analysis, affecting the synthesis of natural products, medicines and materials. The oxidation of allylic systems has played a prominent role in this context as possibly the most widely applied C-H functionalization, owing to the utility of enones and allylic alcohols as versatile intermediates, and their prevalence in natural and unnatural materials. Allylic oxidations have featured in hundreds of syntheses, including some natural product syntheses regarded as “classics”. Despite many attempts to improve the efficiency and practicality of this transformation, the majority of conditions still use highly toxic reagents (based around toxic elements such as chromium or selenium) or expensive catalysts (such as palladium or rhodium). These requirements are problematic in industrial settings; currently, no scalable and sustainable solution to allylic oxidation exists. This oxidation strategy is therefore rarely used for large-scale synthetic applications, limiting the adoption of this retrosynthetic strategy by industrial scientists. Here we describe an electrochemical C-H oxidation strategy that exhibits broad substrate scope, operational simplicity and high chemoselectivity. It uses inexpensive and readily available materials, and represents a scalable allylic C-H oxidation (demonstrated on 100 grams), enabling the adoption of this C-H oxidation strategy in large-scale industrial settings without substantial environmental impact.

Valorization of CH4 emissions into high-added-value products: Assessing the production of ectoine coupled with CH4 abatement.

PubMed

Cantera, Sara; Lebrero, Raquel; Sadornil, Lidia; García-Encina, Pedro A; Muñoz, Raúl

2016-11-01

This study assessed an innovative strategy for the valorization of dilute methane emissions based on the bio-conversion of CH4 (the second most important greenhouse gas (GHG)) into ectoine by the methanotrophic ectoine-producing strain Methylomicrobium alcaliphilum 20 Z. The influence of CH4 (2-20%), Cu(2+) (0.05-50 μM) and NaCl (0-9%) concentration as well as temperature (25-35 °C) on ectoine synthesis and specific CH4 biodegradation rate was evaluated for the first time. Concentrations of 20% CH4 (at 3% NaCl, 0.05 μM Cu(2+), 25 °C) and 6% NaCl (at 4% CH4, 0.05 μM Cu(2+), 25 °C) supported the maximum intra-cellular ectoine production yield (31.0 ±1.7 and 66.9 ±4.2 mg g biomass(-1), respectively). On the other hand, extra-cellular ectoine concentrations of up to 4.7 ± 0.1 mg L(-1) were detected at high Cu(2+)concentrations (50 μM), despite this methanotroph has not been previously classified as an ectoine-excreting strain. This research demonstrated the feasibility of the bio-conversion of dilute emissions of methane into high-added value products in an attempt to develop a sustainable GHG bioeconomy. Copyright © 2016 Elsevier Ltd. All rights reserved.

Satellite Boreal Measurements over Alaska and Canada During June-July 2004: Simultaneous Measurements of Upper Tropospheric CO, C2H6, HCN, CH3Cl, CH4, C2H2, CH2OH, HCOOH, OCS, and SF6 Mixing Ratios

NASA Technical Reports Server (NTRS)

Rinsland, Curtis P.; Dufour, Gaelle; Boone, Chris D.; Bernath, Peter F.; Chiou, Linda; Coheur, Pierre-Francois; Turquety, Solene; Clerbaux, Cathy

2007-01-01

Simultaneous ACE (Atmospheric Chemistry Experiment) upper tropospheric CO, C2H6, HCN, CH3Cl, CH4 , C2H2 , CH30H, HCOOH, and OCS measurements show plumes up to 185 ppbv (10 (exp -9) per unit volume) for CO, 1.36 ppbv for C2H6, 755 pptv (10(exp -12) per unit volume) for HCN, 1.12 ppbv for CH3C1, 1.82 ppmv, (10(exp -6) per unit volume) for CH4, 0.178 ppbv for C2H2, 3.89 ppbv for CH30H, 0.843 ppbv for HCOOH, and 0.48 ppbv for OCS in western Canada and Alaska at 50 deg N-68 deg N latitude between 29 June and 23 July 2004. Enhancement ratios and emission factors for HCOOH, CH30H, HCN, C2H6, and OCS relative to CO at 250-350 hPa are inferred from measurements of young plumes compared with lower mixing ratios assumed to represent background conditions based on a CO emission factor derived from boreal measurements. Results are generally consistent with the limited data reported for various vegetative types and emission phases measured in extratropical forests including boreal forests. The low correlation between fire product emission mixing ratios and the S176 mixing ratio is consistent with no significant SF6 emissions from the biomass fires.

Hydrothermal plumes in the Gulf of Aden, as characterized by light transmission, Mn, Fe, CH4 and δ13C-CH4 anomalies

NASA Astrophysics Data System (ADS)

Gamo, Toshitaka; Okamura, Kei; Hatanaka, Hiroshi; Hasumoto, Hiroshi; Komatsu, Daisuke; Chinen, Masakazu; Mori, Mutsumi; Tanaka, Junya; Hirota, Akinari; Tsunogai, Urumu; Tamaki, Kensaku

2015-11-01

We conducted water column surveys to search for hydrothermal plumes over the spreading axes in the Gulf of Aden between 45°35‧E and 52°42‧E. We measured light transmission and chemical tracers Mn, Fe, CH4 and δ13C of CH4 in seawater taken using a CTD-Carrousel multi-sampling system at 12 locations including a control station in the Arabian Sea. We recognized three types of hydrothermal plumes at depths of 650 to 900 m (shallow plumes), 1000 to 1200 m (intermediate plumes), and >1500 m (deep plumes). The shallow plumes were apparently originated from newly discovered twin seamounts (12°03-06‧N and 45°35-41‧E) at the westernmost survey area, where two-dimensional distributions of light transmission and Mn were mapped by tow-yo observations of the CTD-sampling system with an in situ auto-analyzer GAMOS. The maximum concentrations of Mn, Fe, and CH4 of 46 nM, 251 nM, and 15 nM, respectively, were observed for collected seawater within the shallow plumes. The intermediate plumes were characterized by anomalies of light transmission, Mn, Fe, and δ13C of CH4, but by little CH4 anomalies, suggesting that CH4 had been consumed down to the background level during the aging of the plumes. Anomalies of δ3He already reported by the World Ocean Circulation Experiment (WOCE) program exhibited a hydrothermal plume-like peak at 2000 m depth in the Gulf of Aden, which seems to coincide with the deep plumes observed in this study. The endmember δ13C-CH4 values for the shallow and the deep plumes were estimated to be in a range between -10‰ and -15‰, demonstrating that the sources of CH4 are not biogenic but magmatic as similarly observed at sediment-starved mid-oceanic ridges.

Hospital clinical trial: Homeopathy (Agraphis nutans 5CH, Thuya occidentalis 5CH, Kalium muriaticum 9CH and Arsenicum iodatum 9CH) as adjuvant, in children with otitis media with effusion.

PubMed

Pedrero-Escalas, M F; Jimenez-Antolin, J; Lassaletta, L; Diaz-Saez, G; Gavilán, J

2016-09-01

Otitis media with effusion (OME) is the most common cause of paediatric hearing loss. No single treatment has proved its effectiveness. There is a lack of evidence-based medicine studies in the area of homeopathy. A prospective randomized, double blinded interventional placebo control study was conducted. Patients, from 2 months to 12 years, with OME diagnosed by pneumatic otoscopy (PNO) and tympanometry, were randomized into two groups. Both groups received aerosol therapy (mucolytics and corticosteroids). In addition, the experimental group (EG) received homeopathy (Agraphis nutans 5CH, Thuya Occidentalis 5CH, Kalium muriaticum 9CH and Arsenicum iodatum), and the placebo group (PG) placebo, both of them for 3 months. Patients were evaluated by PNO examination and tympanometry at baseline, at 45 and 90 days. 97 patients were enrolled. In the EG, 61.9% of individuals were cured (PNO went from negative in the 1st visit to positive in the 3rd visit) compared with 56.8% of patients treated with placebo. 4.8% of patients in the EG suffered a recurrence (positive PNO in the 2nd visit changed to negative in the 3rd visit) while 11.4% did in the PG. No significant difference was found. Adverse events were distributed similarly, except in the case of upper respiratory tract infections, which were less frequent in EG (3 vs. 13, p: 0.009). The homeopathic scheme used as adjuvant treatment cannot be claimed to be an effective treatment in children with OME. EUDRACT number: 2011-006086-17, PROTOCOL code: 55005646. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Electronic structure, transport, and phonons of SrAg ChF ( Ch = S,Se,Te): Bulk superlattice thermoelectrics

DOE PAGES

Gudelli, Vijay Kumar; Kanchana, V.; Vaitheeswaran, G.; ...

2015-07-15

Here, we report calculations of the electronic structure, vibrational properties, and transport for the p-type semiconductors, SrAg ChF ( Ch = S, Se, and Te). We find soft phonons with low frequency optical branches intersecting the acoustic modes below 50 cm –1, indicative of a material with low thermal conductivity. The bands at and near the valence-band maxima are highly two-dimensional, which leads to high thermopowers even at high carrier concentrations, which is a combination that suggests good thermoelectric performance. These materials may be regarded as bulk realizations of superlattice thermoelectrics.

[CH(3)(CH(2))(11)NH(3)]SnI(3): a hybrid semiconductor with MoO(3)-type tin(II) iodide layers.

PubMed

Xu, Zhengtao; Mitzi, David B

2003-10-20

The organic-inorganic hybrid [CH(3)(CH(2))(11)NH(3)]SnI(3) presents a lamellar structure with a Sn-I framework isotypic to that of MoO(3). The SnI(3)(-) layer consists of edge and corner-sharing SnI(6) octahedra in which one of the six Sn-I bonds is distinctly elongated (e.g., 3.62 A), indicating lone-pair stereoactivity for the Sn(II) atom. The overall electronic character remains comparable with that of the well-studied SnI(4)(2)(-)-based perovskite semiconductors, such as [CH(3)(CH(2))(11)NH(3)](2)SnI(4), with a red-shifted and broadened exciton peak associated with the band gap, apparently due to the increased dimensionality of the Sn-I framework. The title compound offers, aside from the hybrid perovskites, a new type of solution-processable Sn-I network for potential applications in semiconductive devices.

The addition of iodine to tetramethylammonium iodide

USGS Publications Warehouse

Foote, H.W.; Fleischer, M.

1953-01-01

The system tetramethylammonium iodide-iodine-toluene has been studied by the solubility method at 6 and at 25??. The compounds (CH3)4NI3, (CH3)4NI5 and (CH3)4NI11 were found to be stable phases at both temperatures. In addition, the compound (CH3)4NI10 was found at 6?? and the compound (CH3)4NI9 at 25??. The dissociation pressures of the compounds at these temperatures were calculated from the solubility data.

Biologic properties of a CH2 domain-deleted recombinant immunoglobulin.

PubMed

Slavin-Chiorini, D C; Horan Hand, P H; Kashmiri, S V; Calvo, B; Zaremba, S; Schlom, J

1993-01-02

Monoclonal antibody (MAb) B72.3 reacts with TAG-72, a high-molecular-weight mucin expressed on several types of human carcinoma, and is currently being used in clinical trials for the diagnosis and therapy of human carcinoma. An expression construct containing cDNA encoding an immunoglobulin (Ig) heavy chain, with the variable region of murine MAb B72.3 and a human Ig constant region with a deletion of the CH2 domain, was generated. Immunoglobulin from the transfectoma with the highest expression of the TAG-72 immunoreactive antibody was designated MAb chimeric (c) B72.3 delta CH2. The pharmacokinetics of serum clearance of iodine-labeled MAbs cB72.3 delta CH2 and the intact cB72.3 were compared in athymic mice. By 24 hr, less than 1% of the cB72.3 delta CH2 was left in the plasma, while 36% of the cB72.3 still remained. The T1/2 alpha values of the cB72.3 delta CH2 and cB72.3 MAbs were 1.7 and 2.4 hr, respectively. The T1/2 beta values were 7.8 hr for the domain-deleted cMAb and 48.9 hr for cB72.3. Biodistribution studies in athymic mice bearing LS-174T xenografts showed a reduction in the percentage of injected dose per gram in tumor with 131I-cB72.3 delta CH2; however, the 131I-cB72.3 delta CH2 both localized to tumors faster and cleared from the blood faster than the 125I-cB72.3 MAb. Only trace amounts of the 131I-cB72.3 delta CH2 were detected in normal tissues, including kidney. The faster clearance rate, more rapid tumor targeting and lack of metabolic uptake in normal tissues demonstrated with the iodine-labeled CH2 domain-deleted cMAb may be an advantage for certain clinical protocols.

CH-47F Improved Cargo Helicopter (CH-47F)

DTIC Science & Technology

2015-12-01

Confidence Level Confidence Level of cost estimate for current APB: 50% The Confidence Level of the CH-47F APB cost estimate, which was approved on April...M) Initial PAUC Development Estimate Changes PAUC Production Estimate Econ Qty Sch Eng Est Oth Spt Total 10.316 -0.491 3.003 -0.164 2.273 7.378...SAR Baseline to Current SAR Baseline (TY $M) Initial APUC Development Estimate Changes APUC Production Estimate Econ Qty Sch Eng Est Oth Spt Total

Microheterogeneity in CH3OH/CD3OH mixture

NASA Astrophysics Data System (ADS)

Wrzeszcz, Władysław; Mazurek, Sylwester; Szostak, Roman; Tomza, Paweł; Czarnecki, Mirosław A.

2018-01-01

Recently, we demonstrated the presence of microheterogeneity in binary mixtures of unlike alcohols. [RSC Adv. 2016, 6, 37195-37202] The aim of this work was examination if this phenomenon occurs also in the mixture of very similar alcohols like CH3OH and CD3OH. Theoretical calculations suggest that the isotopic substitution in methyl group influences properties of the OH group. Hence, one can expect that this effect may lead to partial separation of CH3OH and CD3OH at a molecular level and it contributes to deviation from the ideal mixture. This work evidences that CH3OH/CD3OH mixture also deviates from the ideal one, but the extent of this deviation is much smaller as compared with the mixtures of other alcohols. It is of particular note that this deviation results mainly from the difference between the CH3 and CD3 groups, while the contribution from the OH groups is small. The structure of CH3OH/CD3OH mixture at a molecular level is similar to the structure of binary mixtures of other alcohols. The mixture is composed of the homoclusters of both alcohols and the mixed clusters. The homoclusters existing in the mixture are similar to those present in bulk alcohols. The highest population of the heteroclusters and the largest deviation from the ideal mixture were observed at equimolar mixture. Both the experimental and theoretical results reveal that in CH3OH/CD3OH mixture dominate the cyclic tetramers and larger clusters, while the population of the linear clusters is negligible. Though the extent and strength of hydrogen bonding in both alcohols are the same, the position and intensity of the 2ν(OH) band for CH3OH and CD3OH are different. We propose possible explanation of this observation.

Preliminary assignments of 2 ν 3 - ν 4 hot band of 12 CH 4 in the 2 μm transparency window from long-path FTS spectra

NASA Astrophysics Data System (ADS)

Nikitin, A. V.; Daumont, L.; Thomas, X.; Régalia, L.; Rey, M.; Tyuterev, Vl. G.; Brown, L. R.

2011-07-01

New measurements and assignments for the rovibrational transitions of the hot band 2 v3- v4 of 12CH 4 are reported from 4600 to 4880 cm -1 and refer to lower part of the 2 μm methane transparency window. Three long-path spectra were recorded with a Fourier transform spectrometer (FTS) in Reims using an L = 1603 m absorption path length at 1, 7, 34 h Pa for the natural samples of CH 4; a spectrum of enriched 13CH 4 was also used. Assignments were made for 196 lines of 2 v3(F 2,E)- v4. These transitions had an integrated intensity of 5 × 10 -24 cm/molecule at 296 K and improved the overall description of absorption in the 2.1 μm region. The empirical upper state levels of these assignments belong to Tetradecad (4800-6200 cm -1). The new analysis provided much better accuracies of badly blended positions of 2 v3(F 2)-ground state manifolds at 1.66 μm.

ChIP-seq and ChIP-exo profiling of Pol II, H2A.Z, and H3K4me3 in human K562 cells.

PubMed

Mchaourab, Zenab F; Perreault, Andrea A; Venters, Bryan J

2018-03-06

The human K562 chronic myeloid leukemia cell line has long served as an experimental paradigm for functional genomic studies. To systematically and functionally annotate the human genome, the ENCODE consortium generated hundreds of functional genomic data sets, such as chromatin immunoprecipitation coupled to sequencing (ChIP-seq). While ChIP-seq analyses have provided tremendous insights into gene regulation, spatiotemporal insights were limited by a resolution of several hundred base pairs. ChIP-exonuclease (ChIP-exo) is a refined version of ChIP-seq that overcomes this limitation by providing higher precision mapping of protein-DNA interactions. To study the interplay of transcription initiation and chromatin, we profiled the genome-wide locations for RNA polymerase II (Pol II), the histone variant H2A.Z, and the histone modification H3K4me3 using ChIP-seq and ChIP-exo. In this Data Descriptor, we present detailed information on parallel experimental design, data generation, quality control analysis, and data validation. We discuss how these data lay the foundation for future analysis to understand the relationship between the occupancy of Pol II and nucleosome positions at near base pair resolution.

Experimental binding energies for the metal complexes [Mg(CH3OH)n](2+), [Ca(CH3OH)n](2+), and [Sr(CH3OH)n](2+) for n in the range 4-20.

PubMed

Bruzzi, E; Stace, A J

2014-10-09

A supersonic source of clusters has been used to prepare neutral complexes of methanol in association with an alkaline earth metal atom. From these complexes the following metal-containing dications have been generated through electron ionization: [Mg(CH3OH)n](2+), [Ca(CH3OH)n](2+), and [Sr(CH3OH)n](2+), and for n in the range 4-20, kinetic energy release measurements following the evaporation of a single molecule have been undertaken using a high resolution mass spectrometer. Using finite heat bath theory, these data have been transformed into binding energies for individual methanol molecules attached to each of the three cluster systems. In the larger complexes (n > 6) the results exhibit a consistent trend, whereby the experimental binding energy data for all three metal ions are similar, suggesting that the magnitude of the charge rather than charge density influences the strength of the interaction. From a comparison with data recorded previously for (CH3OH)nH(+) it is found that the 2+ charge on a metal ion has an effect on the binding energy of molecules in complexes containing up to 20 solvent molecules. The results recorded for [Ca(CH3OH)n](2+) show evidence of a very marked transition between n = 6 and 7, which is thought to coincide with the completion of a primary solvation shell and the onset of molecules starting to occupy a second and most probably a third shell.

Chætognath transcriptome reveals ancestral and unique features among bilaterians

PubMed Central

Marlétaz, Ferdinand; Gilles, André; Caubit, Xavier; Perez, Yvan; Dossat, Carole; Samain, Sylvie; Gyapay, Gabor; Wincker, Patrick; Le Parco, Yannick

2008-01-01

Background The chætognaths (arrow worms) have puzzled zoologists for years because of their astonishing morphological and developmental characteristics. Despite their deuterostome-like development, phylogenomic studies recently positioned the chætognath phylum in protostomes, most likely in an early branching. This key phylogenetic position and the peculiar characteristics of chætognaths prompted further investigation of their genomic features. Results Transcriptomic and genomic data were collected from the chætognath Spadella cephaloptera through the sequencing of expressed sequence tags and genomic bacterial artificial chromosome clones. Transcript comparisons at various taxonomic scales emphasized the conservation of a core gene set and phylogenomic analysis confirmed the basal position of chætognaths among protostomes. A detailed survey of transcript diversity and individual genotyping revealed a past genome duplication event in the chætognath lineage, which was, surprisingly, followed by a high retention rate of duplicated genes. Moreover, striking genetic heterogeneity was detected within the sampled population at the nuclear and mitochondrial levels but cannot be explained by cryptic speciation. Finally, we found evidence for trans-splicing maturation of transcripts through splice-leader addition in the chætognath phylum and we further report that this processing is associated with operonic transcription. Conclusion These findings reveal both shared ancestral and unique derived characteristics of the chætognath genome, which suggests that this genome is likely the product of a very original evolutionary history. These features promote chætognaths as a pivotal model for comparative genomics, which could provide new clues for the investigation of the evolution of animal genomes. PMID:18533022

The Infrared Spectra of Polycyclic Aromatic Hydrocarbons with Excess Peripheral H Atoms (Hn-PAHs) and their Relation to the 3.4 and 6.9 µm PAH Emission Features

PubMed Central

Sandford, Scott A.; Bernstein, Max P.; Materese, Christopher K.

2015-01-01

Polycyclic aromatic hydrocarbons (PAHs) are likely responsible for the family of infrared emission features seen in a wide variety of astrophysical environments. A potentially important subclass of these materials are PAHs whose edges contain excess H atoms (Hn-PAHs). This type of compound may be present in space, but it has been difficult to assess this possibility because of a lack of suitable laboratory spectra to assist with analysis of astronomical data. We present 4000-500 cm−1 (2.5–20 µm) infrared spectra of 23 Hn-PAHs and related molecules isolated in argon matrices under conditions suitable for interpretation of astronomical data. Spectra of molecules with mixed aromatic and aliphatic domains show characteristics that distinguish them from fully aromatic PAH equivalents. Two major changes occur as PAHs become more hydrogenated: (1) aromatic C-H stretching bands near 3.3 µm weaken and are replaced with stronger aliphatic bands near 3.4 µm, and (2) aromatic C-H out-of-plane bending mode bands in the 11–15 µm region shift and weaken concurrent with growth of a strong aliphatic -CH2-deformation mode near 6.9 µm. Implications for interpreting astronomical spectra are discussed with emphasis on the 3.4 and 6.9 µm features. Laboratory data is compared with emission spectra from IRAS 21282+5050, an object with normal PAH emission features, and IRAS 22272+5435 and IRAS 0496+3429, two protoplanetary nebulae with abnormally large 3.4 µm features. We show that ‘normal’ PAH emission objects contain relatively few Hn-PAHs in their emitter populations, but less evolved protoplanetary nebulae may contain significant abundances of these molecules. PMID:26435553

High-resolution sub-Doppler infrared spectroscopy of atmospherically relevant Criegee precursor CH2I radicals: CH2 stretch vibrations and "charge-sloshing" dynamics

NASA Astrophysics Data System (ADS)

Kortyna, A.; Lesko, D. M. B.; Nesbitt, D. J.

2018-05-01

The combination of a pulsed supersonic slit-discharge source and single-mode difference frequency direct absorption infrared spectroscopy permit first high resolution infrared study of the iodomethyl (CH2I) radical, with the CH2I radical species generated in a slit jet Ne/He discharge and cooled to 16 K in the supersonic expansion. Dual laser beam detection and collisional collimation in the slit expansion yield sub-Doppler linewidths (60 MHz), an absolute frequency calibration of 13 MHz, and absorbance sensitivities within a factor of two of the shot-noise limit. Fully rovibrationally resolved direct absorption spectra of the CH2 symmetric stretch mode (ν2) are obtained and fitted to a Watson asymmetric top Hamiltonian with electron spin-rotation coupling, providing precision rotational constants and spin-rotation tensor elements for the vibrationally excited state. Analysis of the asymmetric top rotational constants confirms a vibrationally averaged planar geometry in both the ground- and first-excited vibrational levels. Sub-Doppler resolution permits additional nuclear spin hyperfine structures to be observed, with splittings in excellent agreement with microwave measurements on the ground state. Spectroscopic data on CH2I facilitate systematic comparison with previous studies of halogen-substituted methyl radicals, with the periodic trends strongly correlated with the electronegativity of the halogen atom. Interestingly, we do not observe any asymmetric CH2 stretch transitions, despite S/N ≈ 25:1 on strongest lines in the corresponding symmetric CH2 stretch manifold. This dramatic reversal of the more typical 3:1 antisymmetric/symmetric CH2 stretch intensity ratio signals a vibrational transition moment poorly described by simple "bond-dipole" models. Instead, the data suggest that this anomalous intensity ratio arises from "charge sloshing" dynamics in the highly polar carbon-iodine bond, as supported by ab initio electron differential density plots and

Limitations and possibilities of low cell number ChIP-seq

PubMed Central

2012-01-01

Background Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq) offers high resolution, genome-wide analysis of DNA-protein interactions. However, current standard methods require abundant starting material in the range of 1–20 million cells per immunoprecipitation, and remain a bottleneck to the acquisition of biologically relevant epigenetic data. Using a ChIP-seq protocol optimised for low cell numbers (down to 100,000 cells / IP), we examined the performance of the ChIP-seq technique on a series of decreasing cell numbers. Results We present an enhanced native ChIP-seq method tailored to low cell numbers that represents a 200-fold reduction in input requirements over existing protocols. The protocol was tested over a range of starting cell numbers covering three orders of magnitude, enabling determination of the lower limit of the technique. At low input cell numbers, increased levels of unmapped and duplicate reads reduce the number of unique reads generated, and can drive up sequencing costs and affect sensitivity if ChIP is attempted from too few cells. Conclusions The optimised method presented here considerably reduces the input requirements for performing native ChIP-seq. It extends the applicability of the technique to isolated primary cells and rare cell populations (e.g. biobank samples, stem cells), and in many cases will alleviate the need for cell culture and any associated alteration of epigenetic marks. However, this study highlights a challenge inherent to ChIP-seq from low cell numbers: as cell input numbers fall, levels of unmapped sequence reads and PCR-generated duplicate reads rise. We discuss a number of solutions to overcome the effects of reducing cell number that may aid further improvements to ChIP performance. PMID:23171294

An eight-dimensional quantum dynamics study of the Cl + CH{sub 4}→ HCl + CH{sub 3} reaction

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

Liu, Na; Yang, Minghui, E-mail: yangmh@wipm.ac.cn

2015-10-07

In this work, the later-barrier reaction Cl + CH{sub 4} → HCl + CH{sub 3} is investigated with an eight-dimensional quantum dynamics method [R. Liu et al., J. Chem. Phys. 137, 174113 (2012)] on the ab initio potential energy surface of Czakó and Bowman [J. Chem. Phys. 136, 044307 (2012)]. The reaction probabilities with CH{sub 4} initially in its ground and vibrationally excited states are calculated with a time-dependent wavepacket method. The theoretical integral cross sections (ICSs) are extensively compared with the available experimental measurements. For the ground state reaction, the theoretical ICSs excellently agree with the experimental ones. Themore » good agreements are also achieved for ratios between ICSs of excited reactions. For ICS ratios between various states, the theoretical values are also consistent with the experimental observations. The rate constants over 200-2000 K are calculated and the non-Arrhenius effect has been observed which is coincident with the previous experimental observations and theoretical calculations.« less

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data.

PubMed

Yang, Jian-Hua; Li, Jun-Hao; Jiang, Shan; Zhou, Hui; Qu, Liang-Hu

2013-01-01

Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) represent two classes of important non-coding RNAs in eukaryotes. Although these non-coding RNAs have been implicated in organismal development and in various human diseases, surprisingly little is known about their transcriptional regulation. Recent advances in chromatin immunoprecipitation with next-generation DNA sequencing (ChIP-Seq) have provided methods of detecting transcription factor binding sites (TFBSs) with unprecedented sensitivity. In this study, we describe ChIPBase (http://deepbase.sysu.edu.cn/chipbase/), a novel database that we have developed to facilitate the comprehensive annotation and discovery of transcription factor binding maps and transcriptional regulatory relationships of lncRNAs and miRNAs from ChIP-Seq data. The current release of ChIPBase includes high-throughput sequencing data that were generated by 543 ChIP-Seq experiments in diverse tissues and cell lines from six organisms. By analysing millions of TFBSs, we identified tens of thousands of TF-lncRNA and TF-miRNA regulatory relationships. Furthermore, two web-based servers were developed to annotate and discover transcriptional regulatory relationships of lncRNAs and miRNAs from ChIP-Seq data. In addition, we developed two genome browsers, deepView and genomeView, to provide integrated views of multidimensional data. Moreover, our web implementation supports diverse query types and the exploration of TFs, lncRNAs, miRNAs, gene ontologies and pathways.

Large CH4 production fueled by autochthonous OC in an anoxic sediment

NASA Astrophysics Data System (ADS)

Grasset, Charlotte; Mendonça, Raquel; Villamor Saucedo, Gabriella; Sobek, Sebastian

2017-04-01

River damming and human-induced eutrophication both affect river and lake functioning, increase organic carbon (OC) sedimentation rates and generate anoxic conditions in bottom waters. Under these conditions, OC in sediments is decomposed into CO2 and CH4, a high potential greenhouse gas. It has been shown that the decomposition of land-derived (allochthonous) OC is inhibited at anoxic conditions, compared to OC internally produced (autochthonous). However, the overall extent and end products (CO2 or CH4) of anoxic decomposition remain poorly known for different types of OC, making it difficult to judge the effect of river damming and eutrophication on greenhouse gas emissions from inland waters. We incubated different types of allochthonous OC (terrestrial plants) and autochthonous OC (phytoplankton and aquatic vascular plants) in an anoxic sediment during 130 days. We aimed to test 1) if this addition of relatively fresh OC resulted in an increase of CH4 production and 2) if autochthonous OC would produce more CH4 than allochthonous OC. We assessed the contribution to CH4 production of the different OC sources (i.e. sediment or added OC) with stable isotope measurements. We found that the addition of relatively fresh OC greatly increased CH4 production. Autochthonous OC generally produced more CH4 than allochthonous OC, but the overall extent of CH4 production was highly variable between the different autochthonous OC types. The d13C-CH4 measurements indicated that CH4 originated exclusively from the added OC. We conclude that the production of CH4 is likely to to be high in eutrophic as well as in artificial lakes, especially when these systems have anoxic bottom waters and high internal primary productivity and thus a high supply of autochthonous OC to the sediment. The current expansion of reservoir construction in concert with almost globally prevalent anthropogenic eutrophication are therefore likely to increase CH4 production in inland waters.

Was Early Mars Warmed by CH4?

NASA Astrophysics Data System (ADS)

Justh, H. L.; Kasting, J. F.

2001-12-01

Images from the Mariner, Viking and Mars Global Surveyor missions have shown geologic features on the Martian surface that seem to indicate an earlier period of hydrologic activity. Many researchers have suggested that the early Martian climate was more Earth-like with a Ts of 273 K or higher. The presence of liquid water would require a greenhouse effect much larger than needed at present since S0 is 25% lower 3.8 billion years ago when the channels are thought to have formed. Research into the effects of CO2 clouds upon the climate of early Mars have yielded results that would not effectively warm the surface to the temperature needed to account for the presence of liquid water. Forget and Pierrehumbert (Science, 1997) showed that large crystals of CO2 ice in clouds that form in the upper troposphere would produce a strong warming effect. Obtaining mean surface temperatures above 273 K would require 100% cloud cover, a condition that is unrealistic for early Mars. It has also been shown that any reduction in cloud cover makes it difficult to achieve warm Martian surface temperatures except at high pressures. CO2 clouds could also cool the Martian surface if they were low and optically thick. CO2 ice may be hard to nucleate, leading to the formation of very large particles (Glandorf, private communication). CH4 has been suggested as an important greenhouse gas on the early Earth. This has led us to look at CH4 as a potential solution to the early Mars climate issue. To investigate the possible warming effect of CH4, we utilized a modified, one-dimensional, radiative-convective climate model that has been used in previous studies of the early Martian climate. New calculations of the effects of CH4 upon the early Martian climate will be presented. The use of CH4 to warm the surface of early Mars does not necessarily imply the presence of life on Mars. Abiotic sources of CH4, such as serpentinization of ultramafic rocks, could supply the concentrations needed to warm

Cationic and Neutral Cp*M(NO)(κ2-Ph2PCH2CH2PPh2) Complexes of Molybdenum and Tungsten: Lewis-Acid-Induced Intramolecular C-H Activation.

PubMed

Handford, Rex C; Wakeham, Russell J; Patrick, Brian O; Legzdins, Peter

2017-03-20

Treatment of CH 2 Cl 2 solutions of Cp*M(NO)Cl 2 (Cp* = η 5 -C 5 (CH 3 ) 5 ; M = Mo, W) first with 2 equiv of AgSbF 6 in the presence of PhCN and then with 1 equiv of Ph 2 PCH 2 CH 2 PPh 2 affords the yellow-orange salts [Cp*M(NO)(PhCN)(κ 2 -Ph 2 PCH 2 CH 2 PPh 2 )](SbF 6 ) 2 in good yields (M = Mo, W). Reduction of [Cp*M(NO)(PhCN)(κ 2 -Ph 2 PCH 2 CH 2 PPh 2 )](SbF 6 ) 2 with 2 equiv of Cp 2 Co in C 6 H 6 at 80 °C produces the corresponding 18e neutral compounds, Cp*M(NO)(κ 2 -Ph 2 PCH 2 CH 2 PPh 2 ) which have been isolated as analytically pure orange-red solids. The addition of 1 equiv of the Lewis acid, Sc(OTf) 3 , to solutions of Cp*M(NO)(κ 2 -Ph 2 PCH 2 CH 2 PPh 2 ) at room temperature results in the immediate formation of thermally stable Cp*M(NO→Sc(OTf) 3 )(H)(κ 3 -(C 6 H 4 )PhPCH 2 CH 2 PPh 2 ) complexes in which one of the phenyl substituents of the Ph 2 PCH 2 CH 2 PPh 2 ligands has undergone intramolecular orthometalation. In a similar manner, addition of BF 3 produces the analogous Cp*M(NO→BF 3 )(H)(κ 3 -(C 6 H 4 )PhPCH 2 CH 2 PPh 2 ) complexes. In contrast, B(C 6 F 5 ) 3 forms the 1:1 Lewis acid-base adducts, Cp*M(NO→B(C 6 F 5 ) 3 )(κ 2 -Ph 2 PCH 2 CH 2 PPh 2 ) in CH 2 Cl 2 at room temperature. Upon warming to 80 °C, Cp*Mo(NO→B(C 6 F 5 ) 3 )(κ 2 -Ph 2 PCH 2 CH 2 PPh 2 ) converts cleanly to the orthometalated product Cp*Mo(NO→B(C 6 F 5 ) 3 )(H)(κ 3 -(C 6 H 4 )PhPCH 2 CH 2 PPh 2 ), but Cp*W(NO→B(C 6 F 5 ) 3 )(κ 2 -Ph 2 PCH 2 CH 2 PPh 2 ) generates a mixture of products whose identities remain to be ascertained. Attempts to extend this chemistry to include related Ph 2 PCH 2 PPh 2 compounds have had only limited success. All new complexes have been characterized by conventional spectroscopic and analytical methods, and the solid-state molecular structures of most of them have been established by single-crystal X-ray crystallographic analyses.

Collisional excitation of CH2 rotational/fine-structure levels by helium

NASA Astrophysics Data System (ADS)

Dagdigian, P. J.; Lique, F.

2018-02-01

Accurate determination of the abundance of CH2 in interstellar media relies on both radiative and collisional rate coefficients. We investigate here the rotational/fine-structure excitation of CH2 induced by collisions with He. We employ a recoupling technique to generate fine-structure-resolved cross-sections and rate coefficients from close coupling spin-free scattering calculations. The calculations are based on a recent, high-accuracy CH2-He potential energy surface computed at the coupled clusters level of theory. The collisional cross-section calculations are performed for all fine-structure transitions among the first 22 and 24 energy levels of ortho- and para-CH2, respectively, and for temperatures up to 300 K. As a first application, we simulate the excitation of CH2 in typical molecular clouds. The excitation temperatures of the CH2 lines are found to be small at typical densities of molecular clouds, showing that the non-local thermodynamic equilibrium approach has to be used to analyse interstellar spectra. We also found that the fine-structure lines connected with the 404 - 313 and 505 - 414 rotational transitions show possible maser emissions so that they can be easily seen in emission. These calculations show that CH2 may have to be detected mainly through absorption spectra.

WETTING STIMULATES ATMOSPHERIC CH4 OXIDATION BY ALPINE SOIL (R823442)

EPA Science Inventory

Studies were done to assess the effects of soil moisture manipulations on CH₄ oxidation in soils from a dry alpine tundra site. When water was added to these soils there was a stimulation of CH₄ oxidation. This stimulation of CH₄ oxidation took ti...

Above- and belowground fluxes of CH4 from boreal shrubs and Scots pine

NASA Astrophysics Data System (ADS)

Halmeenmäki, Elisa; Heinonsalo, Jussi; Santalahti, Minna; Putkinen, Anuliina; Fritze, Hannu; Pihlatie, Mari

2016-04-01

Boreal upland forests are considered as an important sink for the greenhouse gas methane (CH4) due to CH4 oxidizing microbes in the soil. However, recent evidence suggests that vegetation can act as a significant source of CH4. Also, preliminary measurements indicate occasional emissions of CH4 above the tree canopies of a boreal forest. Nevertheless, the sources and the mechanisms of the observed CH4 emissions are still mostly unknown. Furthermore, the majority of CH4 flux studies have been conducted with the soil chamber method, thus not considering the role of the vegetation itself. We conducted a laboratory experiment to study separately the above- and belowground CH4 fluxes of bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), heather (Calluna vulgaris), and Scots pine (Pinus sylvestris), which were grown in microcosms. The above- and belowground fluxes of the plants were measured separately, and these fluxes were compared to fluxes of microcosms containing only humus soil. In addition to the flux measurements, we analysed the CH4 producing archaea (methanogens) and the CH4 consuming bacteria (methanotrophs) with the qPCR method to discover whether these microbes contribute to the CH4 exchange from the plant material and the soil. The results of the flux measurements indicate that the humus soil with roots of lingonberry, heather, and Scots pine consume CH4 compared to bare humus soil. Simultaneously, the shoots of heather and Scots pine emit small amounts of CH4. We did not find detectable amounts of methanogens from any of the samples, suggesting the produced CH4 could be of non-microbial origin, or produced by very small population of methanogens. Based on the first preliminary results, methanotrophs were present in all the studied plant species, and especially in high amounts in the rooted soils, thus implying that the methanotrophs could be responsible of the CH4 uptake in the root-soil systems.

A Time-Dependent Quantum Dynamics Study of the H2 + CH3 yields H + CH4 Reaction

NASA Technical Reports Server (NTRS)

Wang, Dunyou; Kwak, Dochan (Technical Monitor)

2002-01-01

We present a time-dependent wave-packet propagation calculation for the H2 + CH3 yields H + CH4 reaction in six degrees of freedom and for zero total angular momentum. Initial state selected reaction probability for different initial rotational-vibrational states are presented in this study. The cumulative reaction probability (CRP) is obtained by summing over initial-state-selected reaction probability. The energy-shift approximation to account for the contribution of degrees of freedom missing in the 6D calculation is employed to obtain an approximate full-dimensional CRP. Thermal rate constant is compared with different experiment results.

High Resolution Direct Frequency Comb Spectroscopy of Vinyl Bromide (C_2H_3Br) and Nitromethane (CH_3NO_2) in the CH Stretch Region

NASA Astrophysics Data System (ADS)

Changala, Bryan; Spaun, Ben; Patterson, David; Ye, Jun

2016-06-01

We present high resolution rovibrational spectra of buffer gas cooled vinyl bromide (C_2H_3Br) and nitromethane (CH_3NO_2) in the 3 μm CH stretch region, acquired via cavity-enhanced direct frequency comb absorption spectroscopy. The ˜10 K translational and rotational temperatures of the molecular gas, as well as the narrow linewidth of the frequency comb, yield well resolved rotational structure, isotope shifts, and nuclear hyperfine splittings. Given the wide bandwidth of the light source and the long path length of the enhancement cavity, we measure entire vibrational bands in a single shot with high signal-to-noise ratios. We discuss spectra of the entire fundamental CH stretch manifolds of both C_2H_3Br and CH_3NO_2, which provide contrasting examples of rovibrational structure of rigid and non-rigid systems. C_2H_3Br is a relatively normal asymmetric top, exhibiting local perturbations to its rotational structure. Conversely, CH_3NO_2 contains an essentially unhindered methyl rotor. Of particular interest are its quasi-degenerate asymmetric CH stretch modes. Here, one must consider multiple couplings between torsional, rotational, and vibrational angular momentum, leading to qualitatively new level patterns and structure.

Selective Generation of the Radical Cation Isomers [CH3CN](•+) and [CH2CNH](•+) via VUV Photoionization of Different Neutral Precursors and Their Reactivity with C2H4.

PubMed

Polášek, Miroslav; Zins, Emilie-Laure; Alcaraz, Christian; Žabka, Ján; Křížová, Věra; Giacomozzi, Linda; Tosi, Paolo; Ascenzi, Daniela

2016-07-14

Experimental and theoretical studies have been carried out to demonstrate the selective generation of two different C2H3N(+) isomers, namely, the acetonitrile [CH3CN](•+) and the ketenimine [CH2CNH](•+) radical cations. Photoionization and dissociative photoionization experiments from different neutral precursors (acetonitrile and butanenitrile) have been performed using vacuum ultraviolet (VUV) synchrotron radiation in the 10-15 eV energy range, delivered by the DESIRS beamline at the SOLEIL storage ring. For butanenitrile (CH3CH2CH2CN) an experimental ionization threshold of 11.29 ± 0.05 eV is obtained, whereas the appearance energy for the formation of [CH2CNH](•+) fragments is 11.52 ± 0.05 eV. Experimental findings are fully supported by theoretical calculations at the G4 level of theory (ZPVE corrected energies at 0 K), giving a value of 11.33 eV for the adiabatic ionization energy of butanenitrile and an exothermicity of 0.49 for fragmentation into [CH2CNH](•+) plus C2H4, hampered by an energy barrier of 0.29 eV. The energy difference between [CH3CN](•+) and [CH2CNH](•+) is 2.28 eV (with the latter being the lowest energy isomer), and the isomerization barrier is 0.84 eV. Reactive monitoring experiments of the [CH3CN](•+) and [CH2CNH](•+) isomers with C2H4 have been performed using the CERISES guided ion beam tandem mass spectrometer and exploiting the selectivity of ethylene that gives exothermic charge exchange and proton transfer reactions with [CH3CN](•+) but not with [CH2CNH](•+) isomers. In addition, minor reactive channels are observed leading to the formation of new C-C bonds upon reaction of [CH3CN](•+) with C2H4, and their astrochemical implications are briefly discussed.

Interaction of antitumor drug Sn(CH 3) 2Cl 2 with DNA and RNA

NASA Astrophysics Data System (ADS)

Nafisi, Shohreh; Sobhanmanesh, Amir; Esm-Hosseini, Majid; Alimoghaddam, Kamran; Tajmir-Riahi, Heidar Ali

2005-08-01

Sn(CH3)2Cl2 exerts its antitumor activity in a specific way. Unlike anticancer cis-Pt(NH3)2Cl2 drug which binds strongly to the nitrogen atoms of DNA bases, Sn(CH3)2Cl2 shows no major affinity towards base binding. Thus, the mechanism of action by which tinorganometallic compounds exert antitumor activity would be different from that of the cisplatin drug. The aim of this study was to examine the binding of Sn(CH3)2Cl2 with calf thymus DNA and yeast RNA in aqueous solutions at pH 7.1-6.6 with constant concentrations of DNA and RNA and various molar ratios of Sn(CH3)2Cl2/DNA (phosphate) and Sn(CH3)2Cl2/RNA of 1/40, 1/20, 1/10, 1/5. Fourier transform infrared (FTIR) and UV-visible difference spectroscopic methods were used to determine the Sn(CH3)2Cl2 binding mode, binding constant, sequence selectivity and structural variations of Sn(CH3)2Cl2/DNA and Sn(CH3)2Cl2/RNA complexes in aqueous solution. Sn(CH3)2Cl2 hydrolyzes in water to give Sn(CH3)2(OH)2 and [Sn(CH3)2(OH)(H2O)n]+ species. Spectroscopic evidence showed that interaction occurred mainly through (CH3)2Sn(IV) hydroxide and polynucleotide backbone phosphate group with overall binding constant of K(Sn(CH3)2Cl2-DNA)=1.47×105 M-1 and K(Sn(CH3)2Cl2-RNA)=7.33×105 M-1. Sn(CH3)2Cl2 induced no biopolymer conformational changes with DNA remaining in the B-family structure and RNA in A-conformation upon drug complexation.

Palladium-catalysed electrophilic aromatic C-H fluorination

NASA Astrophysics Data System (ADS)

Yamamoto, Kumiko; Li, Jiakun; Garber, Jeffrey A. O.; Rolfes, Julian D.; Boursalian, Gregory B.; Borghs, Jannik C.; Genicot, Christophe; Jacq, Jérôme; van Gastel, Maurice; Neese, Frank; Ritter, Tobias

2018-02-01

Aryl fluorides are widely used in the pharmaceutical and agrochemical industries, and recent advances have enabled their synthesis through the conversion of various functional groups. However, there is a lack of general methods for direct aromatic carbon-hydrogen (C-H) fluorination. Conventional methods require the use of either strong fluorinating reagents, which are often unselective and difficult to handle, such as elemental fluorine, or less reactive reagents that attack only the most activated arenes, which reduces the substrate scope. A method for the direct fluorination of aromatic C-H bonds could facilitate access to fluorinated derivatives of functional molecules that would otherwise be difficult to produce. For example, drug candidates with improved properties, such as increased metabolic stability or better blood-brain-barrier penetration, may become available. Here we describe an approach to catalysis and the resulting development of an undirected, palladium-catalysed method for aromatic C-H fluorination using mild electrophilic fluorinating reagents. The reaction involves a mode of catalysis that is unusual in aromatic C-H functionalization because no organometallic intermediate is formed; instead, a reactive transition-metal-fluoride electrophile is generated catalytically for the fluorination of arenes that do not otherwise react with mild fluorinating reagents. The scope and functional-group tolerance of this reaction could provide access to functional fluorinated molecules in pharmaceutical and agrochemical development that would otherwise not be readily accessible.

E2 and SN2 Reactions of X(-) + CH3CH2X (X = F, Cl); an ab Initio and DFT Benchmark Study.

PubMed

Bento, A Patrícia; Solà, Miquel; Bickelhaupt, F Matthias

2008-06-01

We have computed consistent benchmark potential energy surfaces (PESs) for the anti-E2, syn-E2, and SN2 pathways of X(-) + CH3CH2X with X = F and Cl. This benchmark has been used to evaluate the performance of 31 popular density functionals, covering local-density approximation, generalized gradient approximation (GGA), meta-GGA, and hybrid density-functional theory (DFT). The ab initio benchmark has been obtained by exploring the PESs using a hierarchical series of ab initio methods [up to CCSD(T)] in combination with a hierarchical series of Gaussian-type basis sets (up to aug-cc-pVQZ). Our best CCSD(T) estimates show that the overall barriers for the various pathways increase in the order anti-E2 (X = F) < SN2 (X = F) < SN2 (X = Cl) ∼ syn-E2 (X = F) < anti-E2 (X = Cl) < syn-E2 (X = Cl). Thus, anti-E2 dominates for F(-) + CH3CH2F, and SN2 dominates for Cl(-) + CH3CH2Cl, while syn-E2 is in all cases the least favorable pathway. Best overall agreement with our ab initio benchmark is obtained by representatives from each of the three categories of functionals, GGA, meta-GGA, and hybrid DFT, with mean absolute errors in, for example, central barriers of 4.3 (OPBE), 2.2 (M06-L), and 2.0 kcal/mol (M06), respectively. Importantly, the hybrid functional BHandH and the meta-GGA M06-L yield incorrect trends and qualitative features of the PESs (in particular, an erroneous preference for SN2 over the anti-E2 in the case of F(-) + CH3CH2F) even though they are among the best functionals as measured by their small mean absolute errors of 3.3 and 2.2 kcal/mol in reaction barriers. OLYP and B3LYP have somewhat higher mean absolute errors in central barriers (5.6 and 4.8 kcal/mol, respectively), but the error distribution is somewhat more uniform, and as a consequence, the correct trends are reproduced.

34 CFR 668.34 - Satisfactory academic progress.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 34 Education 3 2013-07-01 2013-07-01 false Satisfactory academic progress. 668.34 Section 668.34... Satisfactory academic progress. (a) Satisfactory academic progress policy. An institution must establish a reasonable satisfactory academic progress policy for determining whether an otherwise eligible student is...

34 CFR 668.34 - Satisfactory academic progress.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 34 Education 3 2014-07-01 2014-07-01 false Satisfactory academic progress. 668.34 Section 668.34... Satisfactory academic progress. (a) Satisfactory academic progress policy. An institution must establish a reasonable satisfactory academic progress policy for determining whether an otherwise eligible student is...

34 CFR 668.34 - Satisfactory academic progress.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 34 Education 3 2012-07-01 2012-07-01 false Satisfactory academic progress. 668.34 Section 668.34... Satisfactory academic progress. (a) Satisfactory academic progress policy. An institution must establish a reasonable satisfactory academic progress policy for determining whether an otherwise eligible student is...

34 CFR 668.34 - Satisfactory academic progress.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 34 Education 3 2011-07-01 2011-07-01 false Satisfactory academic progress. 668.34 Section 668.34... Satisfactory academic progress. (a) Satisfactory academic progress policy. An institution must establish a reasonable satisfactory academic progress policy for determining whether an otherwise eligible student is...

34 CFR 602.34 - Advisory Committee meetings.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 34 Education 3 2010-07-01 2010-07-01 false Advisory Committee meetings. 602.34 Section 602.34 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF POSTSECONDARY EDUCATION, DEPARTMENT OF EDUCATION THE SECRETARY'S RECOGNITION OF ACCREDITING AGENCIES The Recognition...

Rhodium-catalyzed C-H functionalization with N-acylsaccharins.

PubMed

Wu, Hongxiang; Liu, Tingting; Cui, Ming; Li, Yue; Jian, Junsheng; Wang, Hui; Zeng, Zhuo

2017-01-18

A rhodium-catalyzed C-H functionalization with activated amides by decarbonylation has been developed. Notably, this is the first C-H arylation employing N-acylsaccharins as coupling partners to give biaryls in good to excellent yields. The highlight of the work is the high tolerance of functional groups such as formyl, ester, and vinyl and the use of a removable directing group.

Direct production of OH radicals upon CH overtone activation of (CH{sub 3}){sub 2}COO Criegee intermediates

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

Liu, Fang; Beames, Joseph M.; Lester, Marsha I., E-mail: milester@sas.upenn.edu

2014-12-21

Ozonolysis of alkenes, a principle non-photolytic source of atmospheric OH radicals, proceeds through unimolecular decay of energized carbonyl oxide intermediates, known as Criegee intermediates. In this work, cold dimethyl-substituted Criegee intermediates are vibrationally activated in the CH stretch overtone region to drive the 1,4 hydrogen transfer reaction that leads to OH radical products. IR excitation of (CH{sub 3}){sub 2}COO reveals the vibrational states with sufficient oscillator strength, coupling to the reaction coordinate, and energy to surmount the effective barrier (≤ 16.0 kcal mol{sup −1}) to reaction. Insight on the dissociation dynamics is gleaned from homogeneous broadening of the spectral features,more » indicative of rapid intramolecular vibrational energy redistribution and/or reaction, as well as the quantum state distribution of the OH X{sup 2}Π (v = 0) products. The experimental results are compared with complementary electronic structure calculations, which provide the IR absorption spectrum and geometric changes along the intrinsic reaction coordinate. Additional theoretical analysis reveals the vibrational modes and couplings that permit (CH{sub 3}){sub 2}COO to access to the transition state region for reaction. The experimental and theoretical results are compared with an analogous recent study of the IR activation of syn-CH{sub 3}CHOO and its unimolecular decay to OH products [F. Liu, J. M. Beames, A. S. Petit, A. B. McCoy, and M. I. Lester, Science 345, 1596 (2014)].« less

Towards mild metal-catalyzed C-H bond activation.

PubMed

Wencel-Delord, Joanna; Dröge, Thomas; Liu, Fan; Glorius, Frank

2011-09-01

Functionalizing traditionally inert carbon-hydrogen bonds represents a powerful transformation in organic synthesis, providing new entries to valuable structural motifs and improving the overall synthetic efficiency. C-H bond activation, however, often necessitates harsh reaction conditions that result in functional group incompatibilities and limited substrate scope. An understanding of the reaction mechanism and rational design of experimental conditions have led to significant improvement in both selectivity and applicability. This critical review summarizes and discusses endeavours towards the development of mild C-H activation methods and wishes to trigger more research towards this goal. In addition, we examine select examples in complex natural product synthesis to demonstrate the synthetic utility of mild C-H functionalization (84 references). This journal is © The Royal Society of Chemistry 2011

ChEVAS: Combining Suprarenal EVAS with Chimney Technique

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

Torella, Francesco, E-mail: f.torella@liverpool.ac.uk; Chan, Tze Y., E-mail: tze.chan@rlbuht.nhs.uk; Shaikh, Usman, E-mail: usman.shaikh@rlbuht.nhs.uk

2015-10-15

Endovascular sealing with the Nellix{sup ®} endoprosthesis (EVAS) is a new technique to treat infrarenal abdominal aortic aneurysms. We describe the use of endovascular sealing in conjunction with chimney stents for the renal arteries (chEVAS) in two patients, one with a refractory type Ia endoleak and an expanding aneurysm, and one with a large juxtarenal aneurysm unsuitable for fenestrated endovascular repair (EVAR). Both aneurysms were successfully excluded. Our report confirms the utility of chEVAS in challenging cases, where suprarenal seal is necessary. We suggest that, due to lack of knowledge on its durability, chEVAS should only been considered when moremore » conventional treatment modalities (open repair and fenestrated EVAR) are deemed difficult or unfeasible.« less

Estudio del CH interestelar

NASA Astrophysics Data System (ADS)

Olano, C.; Lemarchand, G.; Sanz, A. J.; Bava, J. A.

El objetivo principal de este proyecto consiste en el estudio de la distribución y abundancia del CH en nubes interestelares a través de la observación de las líneas hiperfinas del CH en 3,3 GHz. El CH es una molécula de amplia distribución en el espacio interestelar y una de las pocas especies que han sido observadas tanto con técnicas de radio como ópticas. Desde el punto de vista tecnológico se ha desarrollado un cabezal de receptor que permitirá la realización de observaciones polarimétricas en la frecuencia de 3,3 GHz, con una temperatura del sistema de 60 K y un ancho de banda de 140 MHz, y que será instalado en el foco primario de la antena parabólica del IAR. El cabezal del receptor es capaz de detectar señales polarizadas, separando las componentes de polarización circular derecha e izquierda. Para tal fin el cabezal consta de dos ramas receptoras que amplificarán la señal y la trasladarán a una frecuencia más baja (frecuencia intermedia), permitiendo de esa forma un mejor transporte de la señal a la sala de control para su posterior procesamiento. El receptor además de tener características polarimétricas, podrá ser usado en el continuo y en la línea, utilizando las ventajas observacionales y de procesamiento de señal que actualmente posee el IAR.

Infrared absorption of CH3OSO and CD3OSO radicals produced upon photolysis of CH3OS(O)Cl and CD3OS(O)Cl in p-H2 matrices.

PubMed

Lee, Yu-Fang; Kong, Lin-Jun; Lee, Yuan-Pern

2012-03-28

Irradiation at 239 ± 20 nm of a p-H(2) matrix containing methoxysulfinyl chloride, CH(3)OS(O)Cl, at 3.2 K with filtered light from a medium-pressure mercury lamp produced infrared (IR) absorption lines at 3028.4 (attributable to ν(1), CH(2) antisymmetric stretching), 2999.5 (ν(2), CH(3) antisymmetric stretching), 2950.4 (ν(3), CH(3) symmetric stretching), 1465.2 (ν(4), CH(2) scissoring), 1452.0 (ν(5), CH(3) deformation), 1417.8 (ν(6), CH(3) umbrella), 1165.2 (ν(7), CH(3) wagging), 1152.1 (ν(8), S=O stretching mixed with CH(3) rocking), 1147.8 (ν(9), S=O stretching mixed with CH(3) wagging), 989.7 (ν(10), C-O stretching), and 714.5 cm(-1) (ν(11), S-O stretching) modes of syn-CH(3)OSO. When CD(3)OS(O)Cl in a p-H(2) matrix was used, lines at 2275.9 (ν(1)), 2251.9 (ν(2)), 2083.3 (ν(3)), 1070.3 (ν(4)), 1056.0 (ν(5)), 1085.5 (ν(6)), 1159.7 (ν(7)), 920.1 (ν(8)), 889.0 (ν(9)), 976.9 (ν(10)), and 688.9 (ν(11)) cm(-1) appeared and are assigned to syn-CD(3)OSO; the mode numbers correspond to those used for syn-CH(3)OSO. The assignments are based on the photolytic behavior and a comparison of observed vibrational wavenumbers, infrared intensities, and deuterium isotopic shifts with those predicted with the B3P86∕aug-cc-pVTZ method. Our results extend the previously reported four transient IR absorption bands of gaseous syn-CH(3)OSO near 2991, 2956, 1152, and 994 cm(-1) to 11 lines, including those associated with C-O, O-S, and S=O stretching modes. Vibrational wavenumbers of syn-CD(3)OSO are new. These results demonstrate the advantage of a diminished cage effect of solid p-H(2) such that the Cl atom, produced via UV photodissociation of CH(3)OS(O)Cl in situ, might escape from the original cage to yield isolated CH(3)OSO radicals.

Catalyst- and Reagent-free Electrochemical Azole C-H Amination.

PubMed

Qiu, Youai; Struwe, Julia; Meyer, Tjark H; Oliveira, Joao Carlos Agostinho Carlos Agostinho; Ackermann, Lutz

2018-06-14

Catalyst-, and chemical oxidant-free electrochemical azole C-H aminations were accomplished via cross-dehydrogenative C-H/N-H functionalization. The catalyst-free electrochemical C-H amination proved feasible on azoles with high levels of efficacy and selectivity, avoiding the use of stoichiometric oxidants under ambient conditions. Likewise, the C(sp3)-H nitrogenation proved viable under otherwise identical conditions. The dehydrogenative C-H amination featured ample scope, including cyclic and acyclic aliphatic amines as well as anilines, and employed sustainable electricity as the sole oxidant. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Distinct transport properties of O2 and CH4 across a carbon nanotube

NASA Astrophysics Data System (ADS)

Meng, Xianwen; Wang, Yu; Zhao, Yanjiao; Huang, Jiping

2013-04-01

It is of fundamental importance to investigate either O2 or CH4 molecules across nanochannels in many areas such as breathing or separation. Thus, many researches have focused on such a single type of molecules across nanochannels. However, O2 and CH4 can often appear together and crucially affect human life, say, in a mine. On the basis of molecular dynamics simulations, here we attempt to investigate the mixture of O2 and CH4, in order to identify their different transport properties in a nanochannel. We take a single-walled carbon nanotube (SWCNT) as a model nanochannel, and find that their transport properties are distinctly different. As the concentration of O2 increases up to a high value of 0.8, it is always faster for CH4 molecules to transport across the SWCNT, and the total number of gas molecules transporting across the SWCNT is decreased. Meanwhile, CH4 molecules are always dominant in the SWCNT, and the total number of O2 or CH4 inside the SWCNT is a constant. By calculating the van der Waals interaction between the SWCNT and O2 or CH4, we find that the net interaction between CH4 and the SWCNT is much stronger. Our findings may offer some hints on how to separate CH4 from O2, and/or store CH4 efficiently.

Ion energy distributions and the density of CH3 radicals in a low pressure inductively coupled CH4/H2 plasma used for nanocrystalline diamond deposition

NASA Astrophysics Data System (ADS)

Okada, Katsuyuki; Komatsu, Shojiro; Matsumoto, Seiichiro

2003-11-01

Ion energy distributions (IEDs) and the density of CH3 radicals (n) in a 13.56 MHz radio frequency (rf) low pressure inductively coupled CH4/H2 plasma used for nanocrystalline diamond deposition have been investigated with a quadrupole mass spectrometer. The energy distributions of positive ions were measured in a CH4/H2 plasma with 50 mTorr of the gas pressure at 500 W of the plasma input power, and were compared with those of an Ar plasma. We have found that the IEDs of Ar+, CH4+, and C2H5+ have a nearly monoenergetic peak, and a hump due to a small degree of capacitive coupling. The plasma potentials obtained from the peaks are consistent with the previously reported values measured with a Langmuir probe. On the other hand, the IEDs of H+, H2+, and H3+ have a clear asymmetric double peak due to the modulation of rf driven glow discharge. The n monotonously increases with increasing pressure. The n indicates that CH3 radicals are main precursors for the growth of nanocrystalline diamond. The estimated sticking coefficient of the CH3 radical is comparable with the reported value.

Atmospheric chemistry of cyc-CF2CF2CF2CH=CH-: Kinetics, products, and mechanism of gas-phase reaction with OH radicals, and atmospheric implications

NASA Astrophysics Data System (ADS)

Guo, Qin; Zhang, Ni; Uchimaru, Tadafumi; Chen, Liang; Quan, Hengdao; Mizukado, Junji

2018-04-01

The rate constants for the gas-phase reactions of cyc-CF2CF2CF2CH=CH- with OH radicals were determined by a relative rate method between 253 and 328 K. The rate constant k1 at 298 K was measured to be (1.08 ± 0.04) × 10-13 cm3 molecule-1 s-1, and the Arrhenius expression was k1 = (3.72 ± 0.14) × 10-13 exp [(-370 ± 12)/T]. The atmospheric lifetime of cyc-CF2CF2CF2CH=CH- was calculated to be 107 d. The products and mechanism for the reaction of cyc-CF2CF2CF2CH=CH- with OH radicals were also investigated. CO, CO2, and COF2 were identified as the main carbon-containing products following the OH-initiated reaction. Moreover, the radiative efficiency (RE) was determined to be 0.143 W m-2 ppb-1, and the global warming potentials (GWPs) for 20, 100, and 500 yr were 54, 15, and 4, respectively. The photochemical ozone creation potential of the title compound was estimated to be 1.3.

Replacing -CH2CH2- with -CONH- does not significantly change rates of charge transport through Ag(TS)-SAM//Ga2O3/EGaIn junctions.

PubMed

Thuo, Martin M; Reus, William F; Simeone, Felice C; Kim, Choongik; Schulz, Michael D; Yoon, Hyo Jae; Whitesides, George M

2012-07-04

This paper describes physical-organic studies of charge transport by tunneling through self-assembled monolayers (SAMs), based on systematic variations of the structure of the molecules constituting the SAM. Replacing a -CH(2)CH(2)- group with a -CONH- group changes the dipole moment and polarizability of a portion of the molecule and has, in principle, the potential to change the rate of charge transport through the SAM. In practice, this substitution produces no significant change in the rate of charge transport across junctions of the structure Ag(TS)-S(CH(2))(m)X(CH(2))(n)H//Ga(2)O(3)/EGaIn (TS = template stripped, X = -CH(2)CH(2)- or -CONH-, and EGaIn = eutectic alloy of gallium and indium). Incorporation of the amide group does, however, increase the yields of working (non-shorting) junctions (when compared to n-alkanethiolates of the same length). These results suggest that synthetic schemes that combine a thiol group on one end of a molecule with a group, R, to be tested, on the other (e.g., HS~CONH~R) using an amide-based coupling provide practical routes to molecules useful in studies of molecular electronics.

Ligand-accelerated non-directed C-H functionalization of arenes.

PubMed

Wang, Peng; Verma, Pritha; Xia, Guoqin; Shi, Jun; Qiao, Jennifer X; Tao, Shiwei; Cheng, Peter T W; Poss, Michael A; Farmer, Marcus E; Yeung, Kap-Sun; Yu, Jin-Quan

2017-11-22

The directed activation of carbon-hydrogen bonds (C-H) is important in the development of synthetically useful reactions, owing to the proximity-induced reactivity and selectivity that is enabled by coordinating functional groups. Palladium-catalysed non-directed C-H activation could potentially enable further useful reactions, because it can reach more distant sites and be applied to substrates that do not contain appropriate directing groups; however, its development has faced substantial challenges associated with the lack of sufficiently active palladium catalysts. Currently used palladium catalysts are reactive only with electron-rich arenes, unless an excess of arene is used, which limits synthetic applications. Here we report a 2-pyridone ligand that binds to palladium and accelerates non-directed C-H functionalization with arene as the limiting reagent. This protocol is compatible with a broad range of aromatic substrates and we demonstrate direct functionalization of advanced synthetic intermediates, drug molecules and natural products that cannot be used in excessive quantities. We also developed C-H olefination and carboxylation protocols, demonstrating the applicability of our methodology to other transformations. The site selectivity in these transformations is governed by a combination of steric and electronic effects, with the pyridone ligand enhancing the influence of sterics on the selectivity, thus providing complementary selectivity to directed C-H functionalization.