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Arnbak J, Jacobsen CS, Andrade RB, Guo X, Neergaard-Nielsen JS, Andersen UL, Gehring T. Compact, low-threshold squeezed light source. Opt Express 2019; 27:37877-37885. [PMID: 31878561 DOI: 10.1364/oe.27.037877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/08/2019] [Indexed: 06/10/2023]
Abstract
Strongly squeezed light finds many important applications within the fields of quantum metrology, quantum communication and quantum computation. However, due to the bulkiness and complexity of most squeezed light sources of today, they are still not a standard tool in quantum optics labs. We have taken the first steps in realizing a compact, high-performance 1550 nm squeezing source based on commercially available fiber components combined with a free-space double-resonant parametric down-conversion source. The whole setup, including single-pass second-harmonic generation in a waveguide, fits on a 30 cm×45 cm breadboard and produces 9.3 dB of squeezing at a 5 MHz sideband-frequency. The setup is currently limited by phase noise, but further optimization and development should allow for a 19" sized turn-key squeezing source capable of delivering more than 10 dB of squeezing.
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Tafra E, Culo M, Basletić M, Korin-Hamzić B, Hamzić A, Jacobsen CS. The Hall effect in the organic conductor TTF-TCNQ: choice of geometry for accurate measurements of a highly anisotropic system. J Phys Condens Matter 2012; 24:045602. [PMID: 22214728 DOI: 10.1088/0953-8984/24/4/045602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We have measured the Hall effect on recently synthesized single crystals of the quasi-one-dimensional organic conductor TTF-TCNQ (tetrathiafulvalene-tetracyanoquinodimethane), a well known charge transfer complex that has two kinds of conductive stacks: the donor (TTF) and the acceptor (TCNQ) chains. The measurements were performed in the temperature interval 30 K < T < 300 K and for several different magnetic field and current directions through the crystal. By applying the equivalent isotropic sample approach, we have demonstrated the importance of the choice of optimal geometry for accurate Hall effect measurements. Our results show, contrary to past belief, that the Hall coefficient does not depend on the geometry of measurements and that the Hall coefficient value is approximately zero in the high temperature region (T > 150 K), implying that there is no dominance of either the TTF or the TCNQ chain. At lower temperatures our measurements clearly prove that all three phase transitions of TTF-TCNQ could be identified from Hall effect measurements.
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Affiliation(s)
- E Tafra
- Department of Physics, Faculty of Science, University of Zagreb, Zagreb, Croatia.
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García R, Bælum J, Fredslund L, Santorum P, Jacobsen CS. Influence of temperature and predation on survival of Salmonella enterica serovar Typhimurium and expression of invA in soil and manure-amended soil. Appl Environ Microbiol 2010; 76:5025-31. [PMID: 20562283 PMCID: PMC2916483 DOI: 10.1128/aem.00628-10] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 06/07/2010] [Indexed: 11/20/2022] Open
Abstract
The effects of three temperatures (5, 15, and 25 degrees C) on the survival of Salmonella enterica serovar Typhimurium in topsoil were investigated in small microcosms by three different techniques: plate counting, invA gene quantification, and invA mRNA quantification. Differences in survival were related to the effect of protozoan predation. Tetracycline-resistant Salmonella serovar Typhimurium was inoculated into soil and manure-amended soil at 1.5 x 10(8) cells g soil(-1). Population densities were determined by plate counting and by molecular methods and monitored for 42 days. Simultaneous extraction of RNA and DNA, followed by quantitative PCR, was used to investigate invA gene levels and expression. Analysis by these three techniques showed that Salmonella serovar Typhimurium survived better at 5 degrees C. Comparing DNA and CFU levels, significantly higher values were determined by DNA-based techniques. invA mRNA levels showed a fast decrease in activity, with no detectable mRNA after an incubation period of less than 4 days in any of the soil scenarios. A negative correlation was found between Salmonella serovar Typhimurium CFU levels and protozoan most probable numbers, and we propose the role of the predator-prey interaction as a factor to explain the die-off of the introduced strain by both culture- and DNA quantification-based methods. The results indicate that temperature, manure, and protozoan predation are important factors influencing the survival of Salmonella serovar Typhimurium in soil.
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Affiliation(s)
- R. García
- Geological Survey of Denmark and Greenland (GEUS), DK-1350 Copenhagen, Denmark, Centro de Investigación y Formación Agrarias, Consejería de Desarrollo Rural, Ganadería, Pesca y Biodiversidad, Gobierno de Cantabria, 39600 Muriedas, Cantabria, Spain, University of Copenhagen, Faculty of Life Sciences, DK-1958 Frederiksberg C, Denmark
| | - J. Bælum
- Geological Survey of Denmark and Greenland (GEUS), DK-1350 Copenhagen, Denmark, Centro de Investigación y Formación Agrarias, Consejería de Desarrollo Rural, Ganadería, Pesca y Biodiversidad, Gobierno de Cantabria, 39600 Muriedas, Cantabria, Spain, University of Copenhagen, Faculty of Life Sciences, DK-1958 Frederiksberg C, Denmark
| | - L. Fredslund
- Geological Survey of Denmark and Greenland (GEUS), DK-1350 Copenhagen, Denmark, Centro de Investigación y Formación Agrarias, Consejería de Desarrollo Rural, Ganadería, Pesca y Biodiversidad, Gobierno de Cantabria, 39600 Muriedas, Cantabria, Spain, University of Copenhagen, Faculty of Life Sciences, DK-1958 Frederiksberg C, Denmark
| | - P. Santorum
- Geological Survey of Denmark and Greenland (GEUS), DK-1350 Copenhagen, Denmark, Centro de Investigación y Formación Agrarias, Consejería de Desarrollo Rural, Ganadería, Pesca y Biodiversidad, Gobierno de Cantabria, 39600 Muriedas, Cantabria, Spain, University of Copenhagen, Faculty of Life Sciences, DK-1958 Frederiksberg C, Denmark
| | - C. S. Jacobsen
- Geological Survey of Denmark and Greenland (GEUS), DK-1350 Copenhagen, Denmark, Centro de Investigación y Formación Agrarias, Consejería de Desarrollo Rural, Ganadería, Pesca y Biodiversidad, Gobierno de Cantabria, 39600 Muriedas, Cantabria, Spain, University of Copenhagen, Faculty of Life Sciences, DK-1958 Frederiksberg C, Denmark
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Vinther FP, Brinch UC, Elsgaard L, Fredslund L, Iversen BV, Torp S, Jacobsen CS. Field-scale variation in microbial activity and soil properties in relation to mineralization and sorption of pesticides in a sandy soil. J Environ Qual 2008; 37:1710-8. [PMID: 18689732 DOI: 10.2134/jeq2006.0201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Indexed: 05/26/2023]
Abstract
Pesticides applied to agricultural soils are subject to environmental concerns because leaching to groundwater reservoirs and aquatic habitats may occur. Knowledge of field variation of pesticide-related parameters is required to evaluate the vulnerability of pesticide leaching. The mineralization and sorption of the pesticides glyphosate and metribuzin and the pesticide degradation product triazinamin in a field were measured and compared with the field-scale variation of geochemical and microbiological parameters. We focused on the soil parameters clay and organic carbon (C) content and on soil respiratory and enzymatic processes and microbial biomass. These parameters were measured in soil samples taken at two depths (Ap and Bs horizon) in 51 sampling points from a 4-ha agricultural fine sandy soil field. The results indicated that the spatial variation of the soil parameters, and in particular the content of organic C, had a major influence on the variability of the microbial parameters and on sorption and pesticide mineralization in the soil. For glyphosate, with a co-metabolic pathway for degradation, the mineralization was increased in soils with high microbial activity. The spatial variability, expressed as the CV, was about five times higher in the Bs horizon than in the Ap horizon, and the local-scale variation within 100 m(2) areas were two to three times lower than the field-scale variation within the entire field of about 4 ha.
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Affiliation(s)
- F P Vinther
- Univ. of Aarhus, Faculty of Agricultural Sciences, Inst. of Agroecology and Environment, DK-8830 Tjele, Denmark.
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Fredslund L, Vinther FP, Brinch UC, Elsgaard L, Rosenberg P, Jacobsen CS. Spatial variation in 2-methyl-4-chlorophenoxyacetic acid mineralization and sorption in a sandy soil at field level. J Environ Qual 2008; 37:1918-1928. [PMID: 18689753 DOI: 10.2134/jeq2006.0208] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The phenoxyacetic acid herbicide MCPA (2-methyl-4-chlorophenoxyacetic acid) is frequently detected in groundwater beneath Danish agricultural fields. We investigated spatial variation in microbial MCPA mineralization potential in a flat agricultural field of fine sandy soil (USDA classification: Humic Dystrudept) located on the Yoldia plains of Northern Jutland, Denmark. Samples for determination of MCPA mineralization and sorption were collected from the Ap and Bs horizons at 51 sampling sites located in a 200 x 220 m grid. Spatial variation in sorption was low in both horizons (distribution coefficient, 0.36-4.16 L kg(-1)). Sorption correlated strongly with soil organic carbon content in both horizons (CV, 93 and 83%, respectively) and negatively with soil pH. [Ring-(14)C]-MCPA mineralized readily in the Ap horizon, with 49 to 62% of the (14)C-MCPA being converted to (14)CO(2) during the 67-d incubation period. With the subsoil, mineralization of (14)C-MCPA varied considerably between samples (0.5-72.8%). At neither depth was there correlation between (14)C-MCPA mineralization and sorption, soil pH, organic carbon content, clay content, number of colony-forming units (CFU), pseudomonad CFU, or any of the four microbial activity parameters measured. The presence of microbial genes encoding for the TfdA enzyme was quantified using real-time polymerase chain reaction. No correlation was found between MCPA mineralization potential and the natural background number of tfdA genes present in the soil samples. The degradation kinetics suggests that the high (14)C-MCPA mineralization rate detected in soil samples was linked to growth of the MCPA-degrading soil microbial community.
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Affiliation(s)
- L Fredslund
- Dep. of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Øster Voldgade 10, DK-1350 Copenhagen, Denmark.
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Kristensen KE, Jacobsen CS, Hansen LH, Aamand J, Morgan JAW, Sternberg C, Sørensen SR. Genetic labelling and application of the isoproturon-mineralizing Sphingomonas sp. strain SRS2 in soil and rhizosphere. Lett Appl Microbiol 2006; 43:280-6. [PMID: 16910932 DOI: 10.1111/j.1472-765x.2006.01956.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To construct a luxAB-labelled Sphingomonas sp. strain SRS2 maintaining the ability to mineralize the herbicide isoproturon and usable for monitoring the survival and distribution of strain SRS2 on plant roots in laboratory systems. METHODS AND RESULTS We inserted the mini-Tn5-luxAB marker into strain SRS2 using conjugational mating. In the transconjugant mutants luciferase was produced in varying levels. The mutants showed significant differences in their ability to degrade isoproturon. One luxAB-labelled mutant maintained the ability to mineralize isoproturon and was therefore selected for monitoring colonization of barley roots. CONCLUSIONS We successfully constructed a genetically labelled isoproturon-mineralizing-strain SRS2 and demonstrated its ability to survive in soil and its colonization of rhizosphere. SIGNIFICANCE AND IMPACT OF THE STUDY The construction of a luxAB-labelled strain SRS2 maintaining the degradative ability, provides a powerful tool for ecological studies serving as the basis for evaluating SRS2 as a bioremediation agent.
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Affiliation(s)
- K E Kristensen
- Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen K, Denmark
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Bechgaard K, Carneiro K, Rasmussen FB, Olsen M, Rindorf G, Jacobsen CS, Pedersen HJ, Scott JC. Superconductivity in an organic solid. Synthesis, structure, and conductivity of bis(tetramethyltetraselenafulvalenium) perchlorate, (TMTSF)2ClO4. J Am Chem Soc 2002. [DOI: 10.1021/ja00399a065] [Citation(s) in RCA: 291] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Claessen R, Sing M, Schwingenschlögl U, Blaha P, Dressel M, Jacobsen CS. Spectroscopic signatures of spin-charge separation in the quasi-one-dimensional organic conductor TTF-TCNQ. Phys Rev Lett 2002; 88:096402. [PMID: 11864036 DOI: 10.1103/physrevlett.88.096402] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2001] [Indexed: 05/23/2023]
Abstract
The electronic structure of the quasi-one-dimensional organic conductor TTF-TCNQ is studied by angle-resolved photoelectron spectroscopy (ARPES). The experimental spectra reveal significant discrepancies to band theory. We demonstrate that the measured dispersions can be consistently mapped onto the one-dimensional Hubbard model at finite doping. This interpretation is further supported by a remarkable transfer of spectral weight as a function of temperature. The ARPES data thus show spectroscopic signatures of spin-charge separation on an energy scale of the conduction bandwidth.
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Affiliation(s)
- R Claessen
- Experimentalphysik II, Universität Augsburg, D-86135 Augsburg, Germany
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Andersen SM, Hertz PB, Holst T, Bossi R, Jacobsen CS. Mineralisation studies of 14C-labelled metsulfuron-methyl, tribenuron-methyl, chlorsulfuron and thifensulfuron-methyl in one Danish soil and groundwater sediment profile. Chemosphere 2001; 45:775-782. [PMID: 11695596 DOI: 10.1016/s0045-6535(01)00132-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Bacterial mineralisation of four sulfonylurea herbicides at 20 microg kg(-1) in a sandy soil from nine different depths in a sandy soil horizon (5-780 cm) was investigated in laboratory studies. Metsulfuron-methyl, chlorsulfuron, and tribenuron-methyl were 14C-labelled in the sulfonamide ring, while thifensulfuron-methyl was labelled in the thiophene ring. The highest mineralised amount in 126 days was observed for metsulfuron-methyl (40%) followed by tribenuron-methyl (25%), and thifensulfuron-methyl (11%). Chlorsulfuron showed low mineralisation in all the soils tested (<4%). Mineralisation of the herbicides metsulfuron-methyl and tribenuron-methyl varied according to soil depth (upper profile: 5-70 cm, and lower profile: 165-780 cm) and were proven faster in soil taken from depths 5-7 and 30-35 cm, and slower in depths 45-50 and 70-75 cm. Mineralisation was absent in the lower profile (165-780 cm). As an indicator of microbial activity bacterial counts were taken at the experimental start; these counts grouped in three levels: highest in the surface layer (5-7 cm), slightly lower in the depths 30-75 cm, and lowest in the lower profile (165-780 cm). Residual concentrations of metsulfuron-methyl correlated to the accumulated amount mineralised, with high residual concentrations in soil showing low mineralisation. Also chlorsulfuron showed high residual concentrations with increasing depth in the upper profile, but the relatively high dissipation at 30-35 cm and lower one at 45-50 cm could not be related with the lack of mineralisation. This shows that hydrolysis occurs, but mineralisation of the chloro-substituted sulfonamide is restricted. Tribenuron-methyl and thifensulfuron-methyl could not be detected due to interference with other compounds.
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Affiliation(s)
- S M Andersen
- Department of Geochemistry, Geological Survey of Denmark and Greenland, GEUS, Copenhagen, Denmark
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Andersen SM, Mortensen HS, Bossi R, Jacobsen CS. Isolation and characterisation of Rhodococcus erythropolis TA57 able to degrade the triazine amine product from hydrolysis of sulfonylurea pesticides in soils. Syst Appl Microbiol 2001; 24:262-6. [PMID: 11518330 DOI: 10.1078/0723-2020-00036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We isolated a bacterium capable of metabolising a methylated and methoxylated s-triazine ring as the only nitrogen source. On a weight basis, the s-triazine, commonly named triazine amine (TAM), constitutes approx. half of several sulfonylurea herbicides and is formed after hydrolysis of these herbicides. The isolate, strain TA57 was identified using multi-phasic taxonomy as a gram-positive Rhodococcus erythropolis. Strain TA57 mineralised over 50% 14C-labelled TAM within 4 days in growing cultures using all of the nitrogen for growth. The degradation capacity was found stable in cells grown on either tryptic soy broth agar plates or in minimal medium with NH4+. Among other s-triazines tested, only one other methylated, but de-methoxylated s-triazine amine supported growth. Inoculating 10(6) cells of TA57 per gram of soil (d.w.) resulted in 50% mineralisation of 14C labelled TAM (1 mg kg(-1)) within 25 days, in contrary to the indigenous population that mineralised only 6% in 50 days.
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Affiliation(s)
- S M Andersen
- Department of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen NV
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Fredslund L, Ekelund F, Jacobsen CS, Johnsen K. Development and application of a most-probable-number-pcr assay to quantify flagellate populations in soil samples. Appl Environ Microbiol 2001; 67:1613-8. [PMID: 11282613 PMCID: PMC92777 DOI: 10.1128/aem.67.4.1613-1618.2001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This paper reports on the first successful molecular detection and quantification of soil protozoa. Quantification of heterotrophic flagellates and naked amoebae in soil has traditionally relied on dilution culturing techniques, followed by most-probable-number (MPN) calculations. Such methods are biased by differences in the culturability of soil protozoa and are unable to quantify specific taxonomic groups, and the results are highly dependent on the choice of media and the skills of the microscopists. Successful detection of protozoa in soil by DNA techniques requires (i) the development and validation of DNA extraction and quantification protocols and (ii) the collection of sufficient sequence data to find specific protozoan 18S ribosomal DNA sequences. This paper describes the development of an MPN-PCR assay for detection of the common soil flagellate Heteromita globosa, using primers targeting a 700-bp sequence of the small-subunit rRNA gene. The method was tested by use of gnotobiotic laboratory microcosms with sterile tar-contaminated soil inoculated with the bacterium Pseudomonas putida OUS82 UCB55 as prey. There was satisfactory overall agreement between H. globosa population estimates obtained by the PCR assay and a conventional MPN assay in the three soils tested.
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Affiliation(s)
- L Fredslund
- Geological Survey of Denmark and Greenland, Department of Geochemistry, Thoravej 8, DK-2400 Copenhagen NV, Denmark
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Abstract
In this study, we isolated phenanthrene degraders belonging to Pseudomonas spp. by combining the selective force of two previously described media. The two compounds, sodium lauryl sarcosine and trimethoprim, from the Gould S1 medium, were added to minimal agar plates sprayed with phenanthrene. Pseudomonas spp. that could produce clearing zones were isolated in one step from the rhizosphere without first selecting for Pseudomonas spp. and subsequently screening for degraders or vice versa. Enumeration and isolation of Pseudomonas spp. attached to the rhizosphere showed clear differences between two types of soil. Rhizosphere-attached phenanthrene degraders (from Pseudomonas spp.) were isolated from a former coal gasification site, but were absent in an agricultural soil subjected to organic farming. We isolated 23 phenanthrene degraders producing clearing zones from the rhizosphere of barley roots. All of these 23 isolates (of which 16 were fluorescent in UV light) proved to be members of the Pseudomonas RNA homology group I, on the basis of results of the analytical profile index (API) test system and classic taxonomic tests.
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Affiliation(s)
- S M Andersen
- Department of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen.
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Jacobsen CS, Pedersen HJ, Mortensen K, Bechgaard K. Dibenzo-TTF-dichloro-TCNQ: a quasi-one-dimensional magnetic semiconductor. ACTA ACUST UNITED AC 2000. [DOI: 10.1088/0022-3719/13/18/009] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Jacobsen CS, Pedersen HJ, Mortensen K, Torrance JB, Bechgaard K. An unusual metal-insulator transition: bis(tetramethyltetraselenafulvalenium)-perrhenate (TMTSF2ReO4). ACTA ACUST UNITED AC 2000. [DOI: 10.1088/0022-3719/15/12/014] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Andersen SM, Johnsen K, Sørensen J, Nielsen P, Jacobsen CS. Pseudomonas frederiksbergensis sp. nov., isolated from soil at a coal gasification site. Int J Syst Evol Microbiol 2000; 50 Pt 6:1957-1964. [PMID: 11155968 DOI: 10.1099/00207713-50-6-1957] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phenotypic and genotypic characterization indicated that a group of 29 closely related phenanthrene-degrading bacteria from a coal gasification site in Frederiksberg, Copenhagen, Denmark, belonged to the genus Pseudomonas. The strains were isolated at two sampling occasions 2 years apart. The isolates were phenotypically different from any known species of the genus Pseudomonas and were therefore subject to further identification. Colonies were smooth and pale yellowish and did not produce pigments fluorescent in UV light when grown on King's B agar. Cells were rod-shaped, approximately 0.5-0.8 x 1.5-3.0 microm, and grew at 4 and 30 degrees C, but not 37 degrees C. The bacteria were oxidase- and catalase-positive, accumulated poly-beta-hydroxybutyrate and denitrified, but did not utilize D-xylose. The mean G+C content was 59.6 mol%. Phenotypic data and 16S rDNA sequence data information for Pseudomonas amygdali and Pseudomonas corrugata, and 16S rDNA sequence data for Pseudomonas chlororaphis and Pseudomonas syringae showed close relationships to these strains. However, DNA-DNA hybridization data showed that the isolates belong to a new species, for which the name Pseudomonas frederiksbergensis sp. nov. is proposed. The type strain is JAJ28T (DSM 13022T).
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Tolker-Nielsen T, Brinch UC, Ragas PC, Andersen JB, Jacobsen CS, Molin S. Development and dynamics of Pseudomonas sp. biofilms. J Bacteriol 2000; 182:6482-9. [PMID: 11053394 PMCID: PMC94796 DOI: 10.1128/jb.182.22.6482-6489.2000] [Citation(s) in RCA: 255] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2000] [Accepted: 08/22/2000] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas sp. strain B13 and Pseudomonas putida OUS82 were genetically tagged with the green fluorescent protein and the Discosoma sp. red fluorescent protein, and the development and dynamics occurring in flow chamber-grown two-colored monospecies or mixed-species biofilms were investigated by the use of confocal scanning laser microscopy. Separate red or green fluorescent microcolonies were formed initially, suggesting that the initial small microcolonies were formed simply by growth of substratum attached cells and not by cell aggregation. Red fluorescent microcolonies containing a few green fluorescent cells and green fluorescent microcolonies containing a few red fluorescent cells were frequently observed in both monospecies and two-species biofilms, suggesting that the bacteria moved between the microcolonies. Rapid movement of P. putida OUS82 bacteria inside microcolonies was observed before a transition from compact microcolonies to loose irregularly shaped protruding structures occurred. Experiments involving a nonflagellated P. putida OUS82 mutant suggested that the movements between and inside microcolonies were flagellum driven. The results are discussed in relation to the prevailing hypothesis that biofilm bacteria are in a physiological state different from planktonic bacteria.
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Affiliation(s)
- T Tolker-Nielsen
- Molecular Microbial Ecology Group, Department of Microbiology, The Technical University of Denmark, DK-2800 Lyngby, Denmark
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Ekelund F, Christensen S, Rønn R, Buhl E, Jacobsen CS. An automated technique for most-probable-number (MPN) analysis of densities of phagotrophic protists with lux AB labelled bacteria as growth medium. J Microbiol Methods 1999; 38:177-82. [PMID: 10541430 DOI: 10.1016/s0167-7012(99)00086-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
An automated modification of the most-probable-number (MPN) technique has been developed for enumeration of phagotrophic protozoa. The method is based on detection of prey depletion in micro titre plates rather than on presence of protozoa. A transconjugant Pseudomonas fluorescens DR54 labelled with a luxAB gene cassette was constructed, and used as growth medium for the protozoa in the micro titre plates. The transconjugant produced high amounts of luciferase which was stable and allowed detection for at least 8 weeks. Dilution series of protozoan cultures and soil suspensions were inoculated into micro titre plates amended with a suspension of the transconjugant. After 45 days measurement of light emission allowed detection of individual wells in the titre plates, where protozoan grazing had removed the inoculated bacteria.
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Affiliation(s)
- F Ekelund
- Terrestrial Ecology, Zoological Institute, University of Copenhagen, Denmark.
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Bossi R, Seiden P, Andersen SM, Jacobsen CS, Streibig JC. Analysis of metsulfuron-methyl in soil by liquid chromatography/tandem mass spectrometry. Application to a field dissipation study. J Agric Food Chem 1999; 47:4462-4468. [PMID: 10552834 DOI: 10.1021/jf981280t] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
An analytical method is described for the extraction of metsulfuron-methyl from soil at sub-parts per billion levels (LOQ = 0.2 microgram kg(-1)). The herbicide was quantitatively determined and identified by ESI LC/MS/MS. The method has been applied to a field dissipation study in which metsulfuron-methyl was applied to spring barley at three dosage rates: 4, 8, and 16 g of active ingredient ha(-)(1). The results of 2 years are presented. The dissipation rate of metsulfuron-methyl in topsoil was very rapid, with a calculated half-life of 6.5 days. Laboratory mineralization studies with native soils in contrast to autoclaved soils indicated that microbial degradation of (14)C-labeled metsulfuron-methyl and (14)C-labeled 2-amino-4-methoxy-6-methyl-1,3,5-triazine in soil microcosms is an important factor for the complete degradation of metsulfuron-methyl in the field. However, the mineralization rate of the sulfonamide was much higher.
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Affiliation(s)
- R Bossi
- National Environmental Research Institute, Frederiksborgvej 399, DK-4000 Roskilde, Denmark.
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Bossi R, Vejrup K, Jacobsen CS. Determination of sulfonylurea degradation products in soil by liquid chromatography-ultraviolet detection followed by confirmatory liquid chromatography-tandem mass spectrometry. J Chromatogr A 1999; 855:575-82. [PMID: 10519094 DOI: 10.1016/s0021-9673(99)00721-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A method based on liquid extraction followed by sample enrichment on reversed-phase solid-phase extraction was developed for the extraction of five degradation products of four sulfonylurea herbicides (chlorsulfuron, metsulfuron-methyl, thifensulfuron-methyl and tribenuron-methyl) from soil. The compounds have been quantified by LC-UV and identified by tandem LC-MS with electrospray ionization or atmospheric pressure chemical ionization. The limits of detection for the five compounds were between 10 and 50 micrograms kg-1. The method has been applied to the extraction of soil samples after microbial degradation of sulfonylurea herbicides.
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Affiliation(s)
- R Bossi
- National Environmental Research Institute, Department of Environmental Chemistry, Roskilde, Denmark.
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Johnsen K, Enger O, Jacobsen CS, Thirup L, Torsvik V. Quantitative selective PCR of 16S ribosomal DNA correlates well with selective agar plating in describing population dynamics of indigenous Pseudomonas spp. in soil hot spots. Appl Environ Microbiol 1999; 65:1786-8. [PMID: 10103283 PMCID: PMC91253 DOI: 10.1128/aem.65.4.1786-1788.1999] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We used a quantitative PCR method targeting 16S ribosomal DNA using competitive PCR for specific detection of indigenous Pseudomonas DNA in soil hot spots. The amount of Pseudomonas DNA corresponded to the number of culturable Pseudomonas bacteria on Gould's S1 agar. This represents the first use of PCR for quantification of indigenous bacteria in more than one sample of soil.
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Affiliation(s)
- K Johnsen
- Geological Survey of Denmark and Greenland, Copenhagen, Denmark.
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Abstract
A total of 41 phenanthrene degraders were isolated from a former coal gasification site by using Pseudomonas-selective Gould's S1 medium. All isolates were found to belong to the fluorescent Pseudomonas group and were subjected to characterization by phenotypic methods, including classical taxonomic tests, API 20NE, and Biolog GN, and the strains were further characterized by the genotypic method repetitive extragenic palindromic PCR (REP-PCR). By using classical tests, the population was found to consist of 38 strains belonging to P. fluorescens, 2 P. putida strains, and 1 Pseudomonas sp. Bacteria in phenograms from Biolog GN and REP-PCR data were divided into groups, which were in good agreement with classical test and API 20NE results. We found a nonfluorescent group of 22 bacteria inconsistent with any Pseudomonas sp. in Bergey's Manual of Systematic Bacteriology. The group showed small differences in the genotypic test, indicating that all 22 isolates were not recent clones of the same isolate. Analyses of the nonfluorescent group indicated that it belonged to Pseudomonas, but the group could not be affiliated with P. fluorescens because of differences in DNA-DNA hybridization. Identifications using classical tests and API 20NE were found to correlate, but Biolog GN identifications after 24-h incubation resulted very often in the distantly related P. corrugata. The reproducibilities of individual tests of each phenotypic method were assessed, and low reproducibilities were mainly found to be associated with specific Biolog GN test wells. Classical tests and API 20NE proved to be the best for identification of isolates, whereas Biolog GN and REP-PCR were found to be the best tests for high resolution among these closely related isolates.
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Affiliation(s)
- K Johnsen
- Department of Ecology and Molecular Biology, Royal Veterinary and Agricultural University, Frederiksberg C, Denmark.
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Schiodt NC, Bjornholm T, Bechgaard K, Neumeier JJ, Allgeier C, Jacobsen CS, Thorup N. Structural, electrical, magnetic, and optical properties of bis-benzene-1,2-dithiolato-Au(IV) crystals. Phys Rev B Condens Matter 1996; 53:1773-1778. [PMID: 9983635 DOI: 10.1103/physrevb.53.1773] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Abstract
A magnetic capture-hybridization PCR technique (MCH-PCR) was developed to eliminate the inhibitory effect of humic acids and other contaminants in PCRs targeting specific soil DNA. A single-stranded DNA probe, which was complementary to an internal part of the target gene, was used to coat magnetic beads. After hybridization in a suspension of soil DNA, magnetic extraction of the beads separated the hybrid DNA from all other soil DNA, humic acids, and other interfering soil components. The MCH was followed by PCR amplification of the specific target DNA. In barley rhizosphere soil, detection of a lux gene inserted in a Pseudomonas fluorescens strain could be demonstrated in nonsterile soil samples (0.5 mg). This corresponded to a detection of fewer than 40 bacterial cells per cm of barley root. The MCH-PCR technique greatly improves the current protocols for PCR detection of specific microorganisms or genes in soil because specific target DNA sequences from very small soil samples can be extracted and determined.
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Affiliation(s)
- C S Jacobsen
- Department of Ecology and Molecular Biology, Royal Veterinary and Agricultural University, Frederiksberg C, Copenhagen, Denmark
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Il'ichev EV, Jacobsen CS. Magnetic-flux dynamics of high-Tc superconductors in weak magnetic fields. Phys Rev B Condens Matter 1994; 49:6378-6381. [PMID: 10011637 DOI: 10.1103/physrevb.49.6378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Pedersen JC, Jacobsen CS. Fate of Enterobacter cloacae JP120 and Alcaligenes eutrophus AEO106(pRO101) in soil during water stress: effects on culturability and viability. Appl Environ Microbiol 1993; 59:1560-4. [PMID: 8517752 PMCID: PMC182119 DOI: 10.1128/aem.59.5.1560-1564.1993] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A sandy loam soil near field capacity moisture content (psi = -0.050 MPa) or air dried (psi = -300 MPa) was inoculated with about 3 x 10(7) CFU of Enterobacter cloacae JP120 and Alcaligenes eutrophus AEO106(pRO101) per g and incubated in 40-g portions at 17 degrees C in closed or open Erlenmeyer flasks. In the field-moist soil, selective plating, direct viable counts, and DNA hybridization showed only minor changes in the numbers of E. cloacae and A. eutrophus cells with time (14 days), and the results obtained with the three detection methods generally agreed. In the air-dried soil, the majority of both bacteria were found as intact DNA-carrying cells that were neither culturable nor viable by the methods employed in this study. The numbers of culturable E. cloacae and A. eutrophus cells dropped to 10(5) and 10(2) CFU/g, respectively, 2 h after inoculation. Direct viable counts showed that only about 1% of the cells detected by immunofluorescence microscopy were viable, but a fraction of viable nonculturable cells of both bacteria was present. A. eutrophus did not tolerate desiccation as well as E. cloacae. Only a minor fraction of the two test organisms regained their culturability or viability after rewetting of the air-dried soil; the number of total heterotrophic culturable bacteria, however, increased more than 10-fold and reached 73% of the level found in the field-moist soil at day 14.
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Affiliation(s)
- J C Pedersen
- Department of Marine Ecology and Microbiology, National Environmental Research Institute, Roskilde, Denmark
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Jacobsen CS, Rasmussen OF. Development and application of a new method to extract bacterial DNA from soil based on separation of bacteria from soil with cation-exchange resin. Appl Environ Microbiol 1992; 58:2458-62. [PMID: 16348750 PMCID: PMC195803 DOI: 10.1128/aem.58.8.2458-2462.1992] [Citation(s) in RCA: 138] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new method for the extraction of bacterial DNA from soil has been developed. Soil samples of 50 g were dispersed, and bacteria were released by use of a cation-exchange resin; subsequently, bacteria were separated from soil particles by low-speed centrifugation and lysed with lysozyme and ionic detergent, and the DNA was then purified by CsCl-ethidium bromide equilibrium density centrifugation. The extracted DNA was of high molecular weight and sufficiently pure for restriction enzyme digestion, DNA-DNA hybridization, and amplification by the polymerase chain reaction. The advantages of the new method are that the separation of bacteria from soil is considerably faster than by repeated blending, more samples can be handled, and furthermore no aerosols are formed during separation. Also, we investigated whether the CsCl-ethidium bromide equilibrium density centrifugation could be replaced by purification using Gene-Clean. However, this method produced DNAs which were insufficiently pure for several types of analysis. The new method was used to study survival of a 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading Pseudomonas cepacia DBO1 (pRO101) in unamended soil and in soil amended with 2,4-D. We found that the degrading strain, irrespective of inoculation level, was able to grow to the same high numbers in soil amended with 2,4-D, while the strain in nonamended soil were maintained at the inoculation level. Detection based on DNA extraction and subsequent dot blot DNA-DNA hybridization was in accordance with detection by plating on selective medium.
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Affiliation(s)
- C S Jacobsen
- Department of Marine Ecology and Microbiology, National Environmental Research Institute, Frederiksborgvej 399, DK-4000 Roskilde, and Department of Molecular Food Technology, Biotechnical Institute, Lundtoftevej 100, DK-2800 Lyngby, Denmark
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Abstract
The 2,4-dichlorophenoxyacetic acid (2,4-D) degrading pseudomonad, Pseudomonas cepacia DBO1(pRO101), was inoculated at approximately 10(7) CFU/g into sterile and non-sterile soil amended with 0, 5 or 500 ppm 2,4-D and the survival of the strain was studied for a period of 44 days. In general, the strain survived best in sterile soil. When the sterile soil was amended with 2,4-D, the strain survived at a significantly higher level than in non-amended sterile soil. In non-sterile soil either non-amended or amended with 5 ppm 2,4-D the strain died out, whereas with 500 ppm 2,4-D the strain only declined one order of magnitude through the 44 days. The influence of 0, 0.06, 12 and 600 ppm 2,4-D on short-term (48 h) survival of P. cepacia DBO1(pRO101) inoculated to a level of 6 x 10(4), 6 x 10(6) or 1 x 10(8) CFU/g soil was studied in non-sterile soil. Both inoculum level and 2,4-D concentration were found to have a positive influence on numbers of P. cepacia DBO1(pRO101). At 600 ppm 2,4-D growth was significant irrespective of the inoculation level, and at 12 ppm growth was stimulated at the two lowest inocula levels. P. cepacia DBO1(pRO101) was able to survive for 15 months in sterile buffers kept at room temperature. During this starvation, cells shrunk to about one third the volume of exponentially growing cells.
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Affiliation(s)
- C S Jacobsen
- National Environmental Research Institute, Department of Marine Ecology and Microbiology, Roskilde, Denmark
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Jacobsen CS, Pedersen JC. Mineralization of 2,4-dichlorophenoxyacetic acid (2,4-D) in soil inoculated with Pseudomonas cepacia DBO1(pRO101), Alcaligenes eutrophus AEO106(pRO101) and Alcaligenes eutrophus JMP134(pJP4): effects of inoculation level and substrate concentration. Biodegradation 1992; 2:253-63. [PMID: 1282056 DOI: 10.1007/bf00114557] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mineralization of 2,4-dichlorophenoxyacetic acid (2,4-D) by two Alcaligenes eutrophus strains and one Pseudomonas cepacia strain containing the 2,4-D degrading plasmids pJP4 or pRO101 (= pJP4::Tn1721) was tested in 50 g (wet wt) samples of non-sterile soil. Mineralization was measured as 14C-CO2 evolved during degradation of uniformly-ring-labelled 14C-2,4-D. When the strains were inoculated to a level of approximately 10(8) CFU/g soil, between 20 and 45% of the added 2,4-D (0.05 ppm, 10 ppm or 500 ppm) was mineralized within 72 h. Mineralization of 0.05 ppm and 10 ppm 2,4-D by the two A. eutrophus strains was identical and rapid whereas mineralization by P. cepacia DBO1(pRO101) occurred more slowly. In contrast, mineralization of 500 ppm 2,4-D by the two A. eutrophus strains was very slow whereas mineralization by P. cepacia DBO1 was more rapid. Comparison of 2,4-D mineralization at different levels of inoculation with P. cepacia DBO1(pRO101) (6 x 10(4), 6 x 10(6) and 1 x 10(8) CFU/g soil) revealed that the maximum mineralization rate was reached earlier with the high inoculation levels than with the low level. The kinetics of mineralization were evaluated by nonlinear regression analysis using five different models. The linear or the logarithmic form of a three-half-order model were found to be the most appropriate models for describing 2,4-D mineralization in soil. In the cases in which the logarithmic form of the three-half-order model was the most appropriate model we found, in accordance with the assumptions of the model, a significant growth of the inoculated strains.
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Affiliation(s)
- C S Jacobsen
- National Environmental Research Institute, Department of Marine Ecology and Microbiology, Roskilde, Denmark
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Jacobsen CS, Tanner DB, Williams JM, Geiser U, Wang HH. Electronic structure of some beta -(C10H8S8)2X compounds as studied by infrared spectroscopy. Phys Rev B Condens Matter 1987; 35:9605-9613. [PMID: 9941386 DOI: 10.1103/physrevb.35.9605] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Braude A, Carneiro K, Jacobsen CS, Mortensen K, Turner DJ, Underhill AE. Solid-state properties of one-dimensional metals based on bis(oxalato)platinate anions with divalent cations. Phys Rev B Condens Matter 1987; 35:7835-7846. [PMID: 9941112 DOI: 10.1103/physrevb.35.7835] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Jacobsen CS, Torrance JB. Behavior of charge‐transfer absorption upon passing through the neutral‐ionic phase transition. J Chem Phys 1983. [DOI: 10.1063/1.444530] [Citation(s) in RCA: 113] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Andersen JR, Bechgaard K, Jacobsen CS, Rindorf G, Soling H, Thorup N. The crystal and molecular structure of the organic conductor 2,3,6,7-tetramethyl-1,4,5,8-tetraselenafulvalenium 2,5-dimethyl-7,7,8,8-tetracyano-p-quinodimethanide (TMTSF–DMTCNQ). ACTA ACUST UNITED AC 1978. [DOI: 10.1107/s0567740878006937] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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