Phase Diagram for Light-Induced Superconductivity in κ-(ET)_{2}-X

Resonant optical excitation of certain molecular vibrations in κ-(BEDT-TTF)_{2}Cu[N(CN)_{2}]Br has been shown to induce transient superconductinglike optical properties at temperatures far above equilibrium T_{c}. Here, we report experiments across the bandwidth-tuned phase diagram of this class of materials, and study the Mott insulator κ-(BEDT-TTF)_{2}Cu[N(CN)_{2}]Cl and the metallic compound κ-(BEDT-TTF)_{2}Cu(NCS)_{2}. We find nonequilibrium photoinduced superconductivity only in κ-(BEDT-TTF)_{2}Cu[N(CN)_{2}]Br, indicating that the proximity to the Mott insulating phase and possibly the presence of preexisting superconducting fluctuations are prerequisites for this effect.

Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species

BACKGROUND

Cultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. We report the development of fully annotated, chromosome-scale assemblies for the extant progenitor species of the As- and Cp-subgenomes, Avena atlantica and Avena eriantha respectively. The diploid Avena species serve as important genetic resources for improving common oat's adaptive and food quality characteristics.

RESULTS

The A. atlantica and A. eriantha genome assemblies span 3.69 and 3.78 Gb with an N50 of 513 and 535 Mb, respectively. Annotation of the genomes, using sequenced transcriptomes, identified ~ 50,000 gene models in each species-including 2965 resistance gene analogs across both species. Analysis of these assemblies classified much of each genome as repetitive sequence (~ 83%), including species-specific, centromeric-specific, and telomeric-specific repeats. LTR retrotransposons make up most of the classified elements. Genome-wide syntenic comparisons with other members of the Pooideae revealed orthologous relationships, while comparisons with genetic maps from common oat clarified subgenome origins for each of the 21 hexaploid linkage groups. The utility of the diploid genomes was demonstrated by identifying putative candidate genes for flowering time (HD3A) and crown rust resistance (Pc91). We also investigate the phylogenetic relationships among other A- and C-genome Avena species.

CONCLUSIONS

The genomes we report here are the first chromosome-scale assemblies for the tribe Poeae, subtribe Aveninae. Our analyses provide important insight into the evolution and complexity of common hexaploid oat, including subgenome origin, homoeologous relationships, and major intra- and intergenomic rearrangements. They also provide the annotation framework needed to accelerate gene discovery and plant breeding.

Probing magnetic order and disorder in the one-dimensional molecular spin chains CuF2(pyz) and [Ln(hfac)3(boaDTDA)] n (Ln = Sm, La) using implanted muons

We present the results of muon-spin relaxation ([Formula: see text]SR) measurements on antiferromagnetic and ferromagnetic spin chains. In antiferromagnetic CuF₂(pyz) we identify a transition to long range magnetic order taking place at [Formula: see text] K, allowing us to estimate a ratio with the intrachain exchange of [Formula: see text] and the ratio of interchain to intrachain exchange coupling as [Formula: see text]. The ferromagnetic chain [Sm(hfac)₃(boaDTDA)] _n undergoes an ordering transition at [Formula: see text] K, seen via a broad freezing of dynamic fluctuations on the muon (microsecond) timescale and implying [Formula: see text]. The ordered radical moment continues to fluctuate on this timescale down to 0.3 K, while the Sm moments remain disordered. In contrast, the radical spins in [La(hfac)₃(boaDTDA)] _n remain magnetically disordered down to T  =  0.1 K suggesting [Formula: see text].

Quantum spin liquids unveil the genuine Mott state

The localization of charge carriers by electronic repulsion was suggested by Mott in the 1930s to explain the insulating state observed in supposedly metallic NiO. The Mott metal-insulator transition has been subject of intense investigations ever since^1-3-not least for its relation to high-temperature superconductivity⁴. A detailed comparison to real materials, however, is lacking because the pristine Mott state is commonly obscured by antiferromagnetism and a complicated band structure. Here we study organic quantum spin liquids, prototype realizations of the single-band Hubbard model in the absence of magnetic order. Mapping the Hubbard bands by optical spectroscopy provides an absolute measure of the interaction strength and bandwidth-the crucial parameters that enter calculations. In this way, we advance beyond conventional temperature-pressure plots and quantitatively compose a generic phase diagram for all genuine Mott insulators based on the absolute strength of the electronic correlations. We also identify metallic quantum fluctuations as a precursor of the Mott insulator-metal transition, previously predicted but never observed. Our results suggest that all relevant phenomena in the phase diagram scale with the Coulomb repulsion U, which provides a direct link to unconventional superconductivity in cuprates and other strongly correlated materials.

Pressure-Temperature Phase Diagram Reveals Spin-Lattice Interactions in Co[N(CN)2]2

Diamond anvil cell techniques, synchrotron-based infrared and Raman spectroscopies, and lattice dynamics calculations are combined with prior magnetic property work to reveal the pressure-temperature phase diagram of Co[N(CN)₂]₂. The second-order structural boundaries converge on key areas of activity involving the spin state exposing how the pressure-induced local lattice distortions trigger the ferromagnetic → antiferromagnetic transition in this quantum material.

Transcript Polymorphism Rates in Soybean Seed Tissue Are Increased in a Single Transformant of Glycine max

Transgenic crops have been utilized for decades to enhance agriculture and more recently have been applied as bioreactors for manufacturing pharmaceuticals. Recently, we investigated the gene expression profiles of several in-house transgenic soybean events, finding one transformant group to be consistently different from our controls. In the present study, we examined polymorphisms and sequence variations in the exomes of the same transgenic soybean events. We found that the previously dissimilar soybean line also exhibited markedly increased levels of polymorphisms within mRNA transcripts from seed tissue, many of which are classified as gene expression modifiers. The results from this work will direct future investigations to examine novel SNPs controlling traits of great interest for breeding and improving transgenic soybean crops. Further, this study marks the first work to investigate SNP rates in transgenic soybean seed tissues and demonstrates that while transgenesis may induce abundant unanticipated changes in gene expression and nucleotide variation, phenotypes and overall health of the plants examined remained unaltered.

Population Genomics Related to Adaptation in Elite Oat Germplasm

Six hundred thirty five oat ( L.) lines and 4561 single-nucleotide polymorphism (SNP) loci were used to evaluate population structure, linkage disequilibrium (LD), and genotype-phenotype association with heading date. The first five principal components (PCs) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PCs nor the cross-validation errors from = 1 to 20 model-based analyses suggested a structured population. However, the PC and = 2 model-based analyses supported clustering of lines on spring oat vs. southern United States origin, accounting for 16% of genetic variation ( < 0.0001). Single-locus -statistic () in the highest 1% of the distribution suggested linkage groups that may be differentiated between the two population subgroups. Population structure and kinship-corrected LD of = 0.10 was observed at an average pairwise distance of 0.44 cM (0.71 and 2.64 cM within spring and southern oat, respectively). On most linkage groups LD decay was slower within southern lines than within the spring lines. A notable exception was found on linkage group Mrg28, where LD decay was substantially slower in the spring subpopulation. It is speculated that this may be caused by a heterogeneous translocation event on this chromosome. Association with heading date was most consistent across location-years on linkage groups Mrg02, Mrg12, Mrg13, and Mrg24.

A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

Hexaploid oat ( L., 2 = 6 = 42) is a member of the Poaceae family and has a large genome (∼12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice ( L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.

Paralog analyses reveal gene duplication events and genes under positive selection in Ixodes scapularis and other ixodid ticks

Background

Hard ticks (family Ixodidae) are obligatory hematophagous ectoparasites of worldwide medical and veterinary importance. The haploid genomes of multiple species of ixodid ticks exceed 1 Gbp, prompting questions regarding gene, segmental and whole genome duplication in this phyletic group. The availability of the genome assembly for the black legged tick, Ixodes scapularis, and transcriptome datasets for multiple species of ticks offers an opportunity to assess the contribution of gene duplication to the genome. Here we developed a bioinformatics pipeline to identify and analyze duplicated genes (paralogs) using gene models from the prostriate tick, I. scapularis IscaW1.1 annotation and expressed sequence tags (ESTs) from I. scapularis and the metastriate ticks, Rhipicephalus microplus (southern cattle tick), R. appendiculatus (brown ear tick) and Amblyomma variegatum (tropical bont tick).

Results

Approximately 1-2 % of I. scapularis gene models and 2-14 % of ESTs from the four species represent duplicated genes. The ratio of non-synonymous to synonymous nucleotide substitution rates suggests ~ 25 % of duplicated genes are under positive selection pressure in each species. Analyses of synonymous substitution rates provide evidence for two duplication events in I. scapularis and R. microplus involving several hundred genes. Conservative molecular clock estimates based on synonymous substitution rates for species of Anopheles mosquitoes and the fruit fly, Drosophila melanogaster, suggest these events occurred within the last 50 MYA. Mapping of paralogs to the I. scapularis genome assembly supports tandem, or possibly segmental duplication events.

Conclusions

The present study marks the first genome-level analyses of gene duplication for the Ixodidae and provides insights into mechanisms shaping genome evolution in this group. At least two duplication events involving hundreds of genes may have occurred independently in the lineages prostriata and metastriata, with tandem and segmental duplication the most likely mechanisms for paralog generation. Duplicated genes under positive selection pressure may be linked to emerging functions in the tick and represent important candidates for further study.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2350-2) contains supplementary material, which is available to authorized users.

Microscopic Study of the Fulde-Ferrell-Larkin-Ovchinnikov State in an All-Organic Superconductor

Quasi-two-dimensional superconductors with a sufficiently weak interlayer coupling allow magnetic flux to penetrate in the form of Josephson vortices for in-plane applied magnetic fields. A consequence is the dominance of the Zeeman interaction over orbital effects. In the clean limit, the normal state is favored over superconductivity for fields greater than the paramagnetic limiting field, unless an intermediate, inhomogeneous state is stabilized. Presented here are nuclear magnetic resonance (NMR) studies of the inhomogeneous Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) state for β''-(ET)2SF5CH2CF2SO3. The uniform superconductivity-FFLO transition is identified at an applied field value of 9.3(0.1) T at low temperature (T=130  mK), and evidence for a possible second transition between inhomogeneous states at ∼11  T is presented. The spin polarization distribution inferred from the NMR absorption spectrum compares favorably to a single-Q modulation of the superconducting order parameter.

A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq

BACKGROUND

Soybean (Glycine max) has been bred for thousands of years to produce seeds rich in protein for human and animal consumption, making them an appealing bioreactor for producing valuable recombinant proteins at high levels. However, the effects of expressing recombinant protein at high levels on bean physiology are not well understood. To address this, we investigated whether gene expression within transgenic soybean seed tissue is altered when large amounts of recombinant proteins are being produced and stored exclusively in the seeds. We used RNA-Seq to survey gene expression in three transgenic soybean lines expressing recombinant protein at levels representing up to 1.61 % of total protein in seed tissues. The three lines included: ST77, expressing human thyroglobulin protein (hTG), ST111, expressing human myelin basic protein (hMBP), and 764, expressing a mutant, nontoxic form of a staphylococcal subunit vaccine protein (mSEB). All lines selected for analysis were homozygous and contained a single copy of the transgene.

METHODS

Each transgenic soybean seed was screened for transgene presence and recombinant protein expression via PCR and western blotting.  Whole seed mRNA was extracted and cDNA libraries constructed for Illumina sequencing.  Following alignment to the soybean reference genome, differential gene expression analysis was conducted using edgeR and cufflinks.  Functional analysis of differentially expressed genes was carried out using the gene ontology analysis tool AgriGO.

RESULTS

The transcriptomes of nine seeds from each transgenic line were sequenced and compared with wild type seeds. Native soybean gene expression was significantly altered in line 764 (mSEB) with more than 3000 genes being upregulated or downregulated. ST77 (hTG) and ST111 (hMBP) had significantly less differences with 52 and 307 differentially expressed genes respectively. Gene ontology enrichment analysis found that the upregulated genes in the 764 line were annotated with functions related to endopeptidase inhibitors and protein synthesis, but suppressed expression of genes annotated to the nuclear pore and to protein transport. No significant gene ontology terms were detected in ST77, and only a few genes involved in photosynthesis and thylakoid functions were downregulated in ST111. Despite these differences, transgenic plants and seeds appeared phenotypically similar to non-transgenic controls. There was no correlation between recombinant protein expression level and the quantity of differentially expressed genes detected.

CONCLUSIONS

Measurable unscripted gene expression changes were detected in the seed transcriptomes of all three transgenic soybean lines analyzed, with line 764 being substantially altered. Differences detected at the transcript level may be due to T-DNA insert locations, random mutations following transformation or direct effects of the recombinant protein itself, or a combination of these. The physiological consequences of such changes remain unknown.

Pressure-induced local lattice distortions in α-Co[N(CN)2]2

This work brings together diamond anvil cell techniques, vibrational spectroscopies, and complementary lattice dynamics calculations to investigate pressure-induced local lattice distortions in α-Co[N(CN)2]2. Analysis of mode behavior and displacement patterns reveals a series of pressure-driven transitions that modify the CoN6 counter-rotations, distort the octahedra, and flatten the C-N(ax)-C linkages. These local lattice distortions may be responsible for the low temperature magnetic crossover. We also discuss prospects for negative thermal expansion and show that there is not a straightforward low pressure pathway between the pink α and blue β ambient pressure phases of Co[N(CN)2]2.

Magnetic ordering and charge dynamics in κ-(BEDT-TTF)2Cu[N(CN)2]Cl

The Mott insulator κ-(BEDT-TTF)2Cu[N(CN)2]Cl consists of molecular dimers arranged on an anisotropic triangular lattice. At low temperatures a pronounced dielectric anomaly is observed, and eventually a canted antiferromagnetic ground state forms. Optical spectroscopy clearly rules out charge imbalance and the existence of quantum electric dipoles with a dipolar-spin coupling. Here we suggest a novel form of spin-charge coupling where the prominent in-plane dielectric response in κ-(BEDT-TTF)2Cu[N(CN)2]Cl is explained by short-range discommensurations of the antiferromagnetic phase in the temperature range 30 K < T < 50 K, and by relaxation of charged domain walls in the ferromagnetic structure at lower temperatures.

Electron-phonon and magnetoelastic interactions in ferromagnetic Co[N(CN)2]2

We combined Raman and infrared vibrational spectroscopies with complementary lattice dynamics calculations and magnetization measurements to reveal the dynamic aspects of charge-lattice-spin coupling in Co[N(CN)2]2. Our work uncovers electron-phonon coupling as a magnetic field-driven avoided crossing of the low-lying Co2+ electronic excitation with two ligand phonons and a magnetoelastic effect that signals a flexible local CoN6 environment. Their simultaneous presence indicates the ease with which energy is transferred over multiple length and time scales in this system.

Quantum critical transition amplifies magnetoelastic coupling in Mn[N(CN)2]2

We report the discovery of a magnetic quantum critical transition in Mn[N(CN)(2)](2) that drives the system from a canted antiferromagnetic state to the fully polarized state with amplified magnetoelastic coupling as an intrinsic part of the process. The local lattice distortions, revealed through systematic phonon frequency shifts, suggest a combined MnN(6) octahedra distortion+counterrotation mechanism that reduces antiferromagnetic interactions and acts to accommodate the field-induced state. These findings deepen our understanding of magnetoelastic coupling near a magnetic quantum critical point and away from the static limit.

Statistical issues associated with modeling of synonymous mutation data

The explosion of data in evolutionary bioinformatics has led to sometimes ad hoc, incomplete and even inaccurate data analyses. Taking dS data, namely, data on synonymous substitutions per synonymous sites, we go through a statistical analysis for modeling the time since duplications of genes. We explore the shortcomings of previous analyses, especially with a view towards their effect on inference for the gene duplication process. We present a statistical analysis which respects the assumptions of the models and the integrity of the data, and emphasize that exploratory data analysis, formulation of a data model, its estimation and finally, assessment of the model are important steps in a complete data analysis. Furthermore, for dS data, we develop Bayesian discrete-continuous mixture models and present analyses using two genomes.

Co-expression of soybean Dicer-like genes in response to stress and development

Regulation of gene transcription and post-transcriptional processes is critical for proper development, genome integrity, and stress responses in plants. Many genes involved in the key processes of transcriptional and post-transcriptional regulation have been well studied in model diploid organisms. However, gene and genome duplication may alter the function of the genes involved in these processes. To address this question, we assayed the stress-induced transcription patterns of duplicated gene pairs involved in RNAi and DNA methylation processes in the paleopolyploid soybean. Real-time quantitative PCR and Sequenom MassARRAY expression assays were used to profile the relative expression ratios of eight gene pairs across eight different biotic and abiotic stress conditions. The transcriptional responses to stress for genes involved in DNA methylation, RNAi processing, and miRNA processing were compared. The strongest evidence for pairwise co-expression in response to stresses was exhibited by non-paralogous Dicer-like (DCL) genes GmDCL2a-GmDCL3a and GmDCL1b-GmDCL2b, most profoundly in root tissues. Among homoeologous or paralogous DCL genes, the Dicer-like 2 (DCL2) gene pair exhibited the strongest response to stress and most conserved co-expression pattern. This was surprising because the DCL2 duplication event is more ancient than the other DCL duplications. Possible mechanisms that may be driving the DCL2 co-expression are discussed.

Large-scale development of cost-effective single-nucleotide polymorphism marker assays for genetic mapping in pigeonpea and comparative mapping in legumes

Single-nucleotide polymorphisms (SNPs, >2000) were discovered by using RNA-seq and allele-specific sequencing approaches in pigeonpea (Cajanus cajan). For making the SNP genotyping cost-effective, successful competitive allele-specific polymerase chain reaction (KASPar) assays were developed for 1616 SNPs and referred to as PKAMs (pigeonpea KASPar assay markers). Screening of PKAMs on 24 genotypes [23 from cultivated species and 1 wild species (Cajanus scarabaeoides)] defined a set of 1154 polymorphic markers (77.4%) with a polymorphism information content (PIC) value from 0.04 to 0.38. One thousand and ninety-four PKAMs showed polymorphisms between parental lines of the reference mapping population (C. cajan ICP 28 × C. scarabaeoides ICPW 94). By using high-quality marker genotyping data on 167 F₂ lines from the population, a comprehensive genetic map comprising 875 PKAMs with an average inter-marker distance of 1.11 cM was developed. Previously mapped 35 simple sequence repeat markers were integrated into the PKAM map and an integrated genetic map of 996.21 cM was constructed. Mapped PKAMs showed a higher degree of synteny with the genome of Glycine max followed by Medicago truncatula and Lotus japonicus and least with Vigna unguiculata. These PKAMs will be useful for genetics research and breeding applications in pigeonpea and for utilizing genome information from other legume species.

Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes

A set of 2486 single nucleotide polymorphisms (SNPs) were compiled in chickpea using four approaches, namely (i) Solexa/Illumina sequencing (1409), (ii) amplicon sequencing of tentative orthologous genes (TOGs) (604), (iii) mining of expressed sequence tags (ESTs) (286) and (iv) sequencing of candidate genes (187). Conversion of these SNPs to the cost-effective and flexible throughput Competitive Allele Specific PCR (KASPar) assays generated successful assays for 2005 SNPs. These marker assays have been designated as Chickpea KASPar Assay Markers (CKAMs). Screening of 70 genotypes including 58 diverse chickpea accessions and 12 BC(3) F(2) lines showed 1341 CKAMs as being polymorphic. Genetic analysis of these data clustered chickpea accessions based on geographical origin. Genotyping data generated for 671 CKAMs on the reference mapping population (Cicer arietinum ICC 4958 × Cicer reticulatum PI 489777) were compiled with 317 unpublished TOG-SNPs and 396 published markers for developing the genetic map. As a result, a second-generation genetic map comprising 1328 marker loci including novel 625 CKAMs, 314 TOG-SNPs and 389 published marker loci with an average inter-marker distance of 0.59 cM was constructed. Detailed analyses of 1064 mapped loci of this second-generation chickpea genetic map showed a higher degree of synteny with genome of Medicago truncatula, followed by Glycine max, Lotus japonicus and least with Vigna unguiculata. Development of these cost-effective CKAMs for SNP genotyping will be useful not only for genetics research and breeding applications in chickpea, but also for utilizing genome information from other sequenced or model legumes.

Angle-dependent evolution of the Fulde-Ferrell-Larkin-Ovchinnikov state in an organic superconductor

We report magnetic-field and angular-dependent high-resolution specific-heat measurements of the organic superconductor β''-(BEDT-TTF)2SF5CH2CF2SO3. When the magnetic field is aligned precisely within the conducting BEDT-TTF layer, at low temperatures a clear upturn of the upper critical field beyond the Pauli limit of 9.73 T is observed, hinting at the emergence of a Fulde-Ferrell-Larkin-Ovchinnikov state. This upturn disappears when the field is oriented out of plane by more than ∼0.5  deg. For smaller out-of-plane angles, the specific-heat anomaly at T(c) sharpens and a second peaky phase transition appears within the superconducting state.

Magnetically driven metal-insulator transition in NaOsO3

The metal-insulator transition (MIT) is one of the most dramatic manifestations of electron correlations in materials. Various mechanisms producing MITs have been extensively considered, including the Mott (electron localization via Coulomb repulsion), Anderson (localization via disorder), and Peierls (localization via distortion of a periodic one-dimensional lattice) mechanisms. One additional route to a MIT proposed by Slater, in which long-range magnetic order in a three dimensional system drives the MIT, has received relatively little attention. Using neutron and x-ray scattering we show that the MIT in NaOsO(3) is coincident with the onset of long-range commensurate three dimensional magnetic order. While candidate materials have been suggested, our experimental methodology allows the first definitive demonstration of the long predicted Slater MIT.

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

Pigeonpea is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world. We used the Illumina next-generation sequencing platform to generate 237.2 Gb of sequence, which along with Sanger-based bacterial artificial chromosome end sequences and a genetic map, we assembled into scaffolds representing 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome. Genome analysis predicted 48,680 genes for pigeonpea and also showed the potential role that certain gene families, for example, drought tolerance-related genes, have played throughout the domestication of pigeonpea and the evolution of its ancestors. Although we found a few segmental duplication events, we did not observe the recent genome-wide duplication events observed in soybean. This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries.

Comparative evolution of photosynthetic genes in response to polyploid and nonpolyploid duplication

The likelihood of duplicate gene retention following polyploidy varies by functional properties (e.g. gene ontologies or protein family domains), but little is known about the effects of whole-genome duplication on gene networks related by a common physiological process. Here, we examined the effects of both polyploid and nonpolyploid duplications on genes encoding the major functional groups of photosynthesis (photosystem I, photosystem II, the light-harvesting complex, and the Calvin cycle) in the cultivated soybean (Glycine max), which has experienced two rounds of whole-genome duplication. Photosystem gene families exhibit retention patterns consistent with dosage sensitivity (preferential retention of polyploid duplicates and elimination of nonpolyploid duplicates), whereas Calvin cycle and light-harvesting complex gene families do not. We observed similar patterns in barrel medic (Medicago truncatula), which shared the older genome duplication with soybean but has evolved independently for approximately 50 million years, and in Arabidopsis (Arabidopsis thaliana), which experienced two nested polyploidy events independent from the legume duplications. In both soybean and Arabidopsis, Calvin cycle gene duplicates exhibit a greater capacity for functional differentiation than do duplicates within the photosystems, which likely explains the greater retention of ancient, nonpolyploid duplicates and larger average gene family size for the Calvin cycle relative to the photosystems.

Bandwidth tuning triggers interplay of charge order and superconductivity in two-dimensional organic materials

We observe charge-order fluctuations in the quasi-two-dimensional organic superconductor β''-(BEDT-TTF)2SF5CH2CF2SO3, both by means of vibrational spectroscopy, locally probing the fluctuating charge order, and by investigating the in-plane dynamical response by infrared reflectance spectroscopy. The decrease of the effective electronic interaction in an isostructural metal suppresses both charge-order fluctuations and superconductivity, pointing to their interplay. We compare the results of our experiments with calculations on the extended Hubbard model.

Integration of physical and genetic maps of common bean through BAC-derived microsatellite markers

BACKGROUND

Common bean (Phaseolus vulgaris L.) is the most important legume for direct human consumption and the goal of this study was to integrate a recently constructed physical map for the species with a microsatellite based genetic map using a BAC library from the genotype G19833 and the recombinant inbred line population DOR364 x G19833.

RESULTS

We searched for simple sequence repeats (SSRs) in the 89,017 BAC-end sequences (BES) from the physical map and genetically mapped any polymorphic BES-SSRs onto the genetic map. Among the BES it was possible to identify 623 contig-linked SSRs, most of which were highly AT-rich. A subgroup of 230 di-nucleotide and tri-nucleotide based SSR primer pairs from these BACs was tested on the mapping parents with 176 single copy loci and 114 found to be polymorphic markers. Of these, 99 were successfully integrated into the genetic map. The 99 linkages between the genetic and physical maps corresponded to an equal number of contigs containing a total of 5,055 BAC clones.

CONCLUSIONS

Class II microsatellites were more common in the BES than longer class I microsatellites. Both types of markers proved to be valuable for linking BAC clones to the genetic map and were successfully placed across all 11 linkage groups. The integration of common bean physical and genetic maps is an important part of comparative genome analysis and a prelude to positional cloning of agronomically important genes for this crop.

Integration of physical and genetic maps of common bean through BAC-derived microsatellite markers

Background

Common bean (Phaseolus vulgaris L.) is the most important legume for direct human consumption and the goal of this study was to integrate a recently constructed physical map for the species with a microsatellite based genetic map using a BAC library from the genotype G19833 and the recombinant inbred line population DOR364 × G19833.

Results

We searched for simple sequence repeats (SSRs) in the 89,017 BAC-end sequences (BES) from the physical map and genetically mapped any polymorphic BES-SSRs onto the genetic map. Among the BES it was possible to identify 623 contig-linked SSRs, most of which were highly AT-rich. A subgroup of 230 di-nucleotide and tri-nucleotide based SSR primer pairs from these BACs was tested on the mapping parents with 176 single copy loci and 114 found to be polymorphic markers. Of these, 99 were successfully integrated into the genetic map. The 99 linkages between the genetic and physical maps corresponded to an equal number of contigs containing a total of 5,055 BAC clones.

Conclusions

Class II microsatellites were more common in the BES than longer class I microsatellites. Both types of markers proved to be valuable for linking BAC clones to the genetic map and were successfully placed across all 11 linkage groups. The integration of common bean physical and genetic maps is an important part of comparative genome analysis and a prelude to positional cloning of agronomically important genes for this crop.

Lattice effects and entropy release at the low-temperature phase transition in the spin-liquid candidate kappa-(BEDT-TTF)2Cu2(CN)3

The spin-liquid candidate kappa-(BEDT-TTF)2Cu2(CN)3 has been studied by measuring the uniaxial expansion coefficients alpha(i), the specific heat, and magnetic susceptibility. Special emphasis was placed on the mysterious anomaly around 6 K--a potential spin-liquid instability. Distinct and strongly anisotropic lattice effects have been observed at 6 K, clearly identifying this feature as a second-order phase transition. Owing to the large anomalies in alpha(i), the application of Grüneisen scaling has enabled us to determine the corresponding specific heat contribution and the entropy release. Comparison of the latter with available spin models suggests that spin degrees of freedom alone cannot account for the phase transition. Scenarios involving charge degrees of freedom are discussed.

Magnetoelastic coupling through the antiferromagnet-to-ferromagnet transition of quasi-two-dimensional [Cu(HF2)(pyz)2]BF4 using infrared spectroscopy

We investigated magnetoelastic coupling through the field-driven transition to the fully polarized magnetic state in quasi-two-dimensional [Cu(HF2)(pyz)2]BF4 by magnetoinfrared spectroscopy. This transition modifies out-of-plane ring distortion and bending vibrational modes of the pyrazine ligand. The extent of these distortions increases with the field, systematically tracking the low-temperature magnetization. These distortions weaken the antiferromagnetic spin exchange, a finding that provides important insight into magnetic transitions in other copper halides.

Fractionation of synteny in a genomic region containing tandemly duplicated genes across glycine max, Medicago truncatula, and Arabidopsis thaliana

Extended comparison of gene sequences found on homeologous soybean Bacterial Artificial Chromosomes to Medicago truncatula and Arabidopsis thaliana genomic sequences demonstrated a network of synteny within conserved regions interrupted by gene addition and/or deletions. Consolidation of gene order among all 3 species provides a picture of ancestral gene order. The observation supports a genome history of fractionation resulting from gene loss/addition and rearrangement. In all 3 species, clusters of N-hydroxycinnamoyl/benzoyltransferase genes were identified in tandemly duplicated clusters. Parsimony-based gene trees suggest that the genes within the arrays have independently undergone tandem duplication in each species.

Muon-fluorine entangled states in molecular magnets

The information accessible from a muon-spin relaxation experiment can be limited due to a lack of knowledge of the precise muon stopping site. We demonstrate here the possibility of localizing a spin polarized muon in a known stopping state in a molecular material containing fluorine. The muon-spin precession that results from the entangled nature of the muon spin and surrounding nuclear spins is sensitive to the nature of the stopping site. We use this property to identify three classes of sites that occur in molecular magnets and describe the extent to which the muon distorts its surroundings.

Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing

BACKGROUND

Soybean, Glycine max (L.) Merr., is a well documented paleopolyploid. What remains relatively under characterized is the level of sequence identity in retained homeologous regions of the genome. Recently, the Department of Energy Joint Genome Institute and United States Department of Agriculture jointly announced the sequencing of the soybean genome. One of the initial concerns is to what extent sequence identity in homeologous regions would have on whole genome shotgun sequence assembly.

RESULTS

Seventeen BACs representing approximately 2.03 Mb were sequenced as representative potential homeologous regions from the soybean genome. Genetic mapping of each BAC shows that 11 of the 20 chromosomes are represented. Sequence comparisons between homeologous BACs shows that the soybean genome is a mosaic of retained paleopolyploid regions. Some regions appear to be highly conserved while other regions have diverged significantly. Large-scale "batch" reassembly of all 17 BACs combined showed that even the most homeologous BACs with upwards of 95% sequence identity resolve into their respective homeologous sequences. Potential assembly errors were generated by tandemly duplicated pentatricopeptide repeat containing genes and long simple sequence repeats. Analysis of a whole-genome shotgun assembly of 80,000 randomly chosen JGI-DOE sequence traces reveals some new soybean-specific repeat sequences.

CONCLUSION

This analysis investigated both the structure of the paleopolyploid soybean genome and the potential effects retained homeology will have on assembling the whole genome shotgun sequence. Based upon these results, homeologous regions similar to those characterized here will not cause major assembly issues.

Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing

BACKGROUND

Soybean, Glycine max (L.) Merr., is a well documented paleopolyploid. What remains relatively under characterized is the level of sequence identity in retained homeologous regions of the genome. Recently, the Department of Energy Joint Genome Institute and United States Department of Agriculture jointly announced the sequencing of the soybean genome. One of the initial concerns is to what extent sequence identity in homeologous regions would have on whole genome shotgun sequence assembly.

RESULTS

Seventeen BACs representing approximately 2.03 Mb were sequenced as representative potential homeologous regions from the soybean genome. Genetic mapping of each BAC shows that 11 of the 20 chromosomes are represented. Sequence comparisons between homeologous BACs shows that the soybean genome is a mosaic of retained paleopolyploid regions. Some regions appear to be highly conserved while other regions have diverged significantly. Large-scale "batch" reassembly of all 17 BACs combined showed that even the most homeologous BACs with upwards of 95% sequence identity resolve into their respective homeologous sequences. Potential assembly errors were generated by tandemly duplicated pentatricopeptide repeat containing genes and long simple sequence repeats. Analysis of a whole-genome shotgun assembly of 80,000 randomly chosen JGI-DOE sequence traces reveals some new soybean-specific repeat sequences.

CONCLUSION

This analysis investigated both the structure of the paleopolyploid soybean genome and the potential effects retained homeology will have on assembling the whole genome shotgun sequence. Based upon these results, homeologous regions similar to those characterized here will not cause major assembly issues.

Hydrogen Bonding and Multiphonon Structure in Copper Pyrazine Coordination Polymers

We report a systematic investigation of the temperature-dependent infrared vibrational spectra of a family of chemically related coordination polymer magnets based upon bridging bifluoride (HF(2)-) and terminal fluoride (F-) ligands in copper pyrazine complexes including Cu(HF(2))(pyz)(2)BF(4), Cu(HF(2))(pyz)(2)ClO(4), and CuF(2)(H(2)O)(2)(pyz). We compare our results with several one- and two-dimensional prototype materials including Cu(pyz)(NO(3))(2) and Cu(pyz)(2)(ClO(4))(2). Unusual low-temperature hydrogen bonding, local structural transitions associated with stronger low-temperature hydrogen bonding, and striking multiphonon effects that derive from coupling of an infrared-active fundamental with strong Raman-active modes of the pyrazine building-block molecule are observed. On the basis of the spectroscopic evidence, these interactions are ubiquitous to this family of coordination polymers and may work to stabilize long-range magnetic ordering at low temperature. Similar interactions are likely to be present in other molecule-based magnets.

Specific-heat measurements of the gap structure of the organic superconductors kappa-(ET)2Cu[N(CN)2]Br and kappa-(ET)2Cu(NCS)2

We present high resolution heat capacity measurements of the organic superconductors kappa-(ET)(2)Cu[N(CN)(2)]Br and kappa-(ET)(2)Cu(NCS)(2) in fields up to 14 T. We use the high field data to determine the normal state specific heat and hence extract the behavior of the electronic specific heat C(el) in the superconducting state in zero and finite fields. We find that in both materials for T/T(c) less or similar 0.3, C(el)(H=0) approximately T2 indicating d-wave superconductivity. The data are well described by a strong coupling d-wave model from our base temperature (T/T(c) approximately 0.1) right up to T(c). Our data help to resolve the controversy regarding the order parameter symmetry in these materials.

Persistence to high temperatures of interlayer coherence in an organic superconductor

The interlayer magnetoresistance rho(zz) of the organic metal kappa-(BEDT-TTF)(2)Cu(NCS)(2) is studied in fields of up to 45 T and at temperatures T from 0.5 to 30 K. The peak in rho(zz) seen in in-plane fields, a definitive signature of interlayer coherence, remains to Ts exceeding the Anderson criterion for incoherent transport by a factor approximately 30. Angle-dependent magnetoresistance oscillations are modeled using an approach based on field-induced quasiparticle paths on a 3D Fermi surface, to yield the T dependence of the scattering rate tau(-1). The results suggest that tau(-1) does not vary strongly over the Fermi surface, and that it has a T(2) dependence due to electron-electron scattering.

Characterization of the Crystal and Magnetic Structures of the Mixed-Anion Coordination Polymer Cu(HCO2)(NO3)(pyz) {pyz = Pyrazine} by X-ray Diffraction, ac Magnetic Susceptibility, dc Magnetization, Muon-Spin Relaxation, and Spin Dimer Analysis

The mixed-anion coordination polymer Cu(HCO2)(NO3)(pyz) was synthesized, its crystal structure was determined by X-ray diffraction, and its magnetic structure was characterized by ac susceptibility, dc magnetization, muon-spin relaxation, and spin dimer analysis. The crystal structure consists of five-coordinate Cu2+ ions that are connected through syn-anti bridging mu-HCO2- and mu-pyz ligands to form a highly corrugated two-dimensional layered network. Bulk magnetic measurements show a broad maximum in chi(T) at 6.6 K. The HCO2- and pyz ligands mediate ferromagnetic and antiferromagnetic spin exchange interactions between adjacent Cu2+ ions with the spin exchange parameters J/kB = 8.17 and -5.4 K, respectively (H = -JSigmaSi x Sj). The muon-spin relaxation data show a transition to a long-range magnetic ordering below TN = 3.66(3) K. For T < TN, the M(H) and chi'ac measurements provide evidence for a field-induced spin-flop transition at 15.2 kOe. That Cu(HCO2)(NO3)(pyz) undergoes a long-range magnetic ordering is an unexpected result because the one-dimensional Cu(NO3)2(pyz) and three-dimensional Cu(HCO2)2(pyz) compounds display linear chain antiferromagnetism with no long-range magnetic ordering down to 2 K.

Sequence conservation of homeologous bacterial artificial chromosomes and transcription of homeologous genes in soybean (Glycine max L. Merr.)

The paleopolyploid soybean genome was investigated by sequencing homeologous BAC clones anchored by duplicate N-hydroxycinnamoyl/benzoyltransferase (HCBT) genes. The homeologous BACs were genetically mapped to linkage groups C1 and C2. Annotation of the 173,747- and 98,760-bp BACs showed that gene conservation in both order and orientation is high between homeologous regions with only a single gene insertion/deletion and local tandem duplications differing between the regions. The nucleotide sequence conservation extends into intergenic regions as well, probably due to conserved regulatory sequences. Most of the homeologs appear to have a role in either transcription/DNA binding or cellular signaling, suggesting a potential preference for retention of duplicate genes with these functions. Reverse transcriptase-PCR analysis of homeologs showed that in the tissues sampled, most homeologs have not diverged greatly in their transcription profiles. However, four cases of changes in transcription were identified, primarily in the HCBT gene cluster. Because a mapped locus corresponds to a soybean cyst nematode (SCN) QTL, the potential role of HCBT genes in response to SCN is discussed. These results are the first sequenced-based analysis of homeologous BACs in soybean, a diploidized paleopolyploid.

Lung development in laminin gamma2 deficiency: abnormal tracheal hemidesmosomes with normal branching morphogenesis and epithelial differentiation

Background

Laminin γ2 (Lamc2), one of the polypeptides in laminin-332 (laminin-5), is prominent in the basement membrane of alveolar walls and airways of developing and adult lung. Laminins are important for lung morphogenesis and based on its localization, a function for laminin γ2 in lung development has been hypothesized. Targeted deletion of the laminin γ2 gene in mice results in skin blistering and neonatal death at 3–5 days after birth due to failure to thrive.

Methods

Examination of lung development in Lamc2-/- mice through 1–2 days postnatal was accomplished by morphometric analysis, lung bud culture, electron microscopy, immunohistochemical and immunofluorescence staining.

Results

Compared to littermate controls, Lamc2-/- lungs were similar in morphology during embryonic life. At post-natal day 1–2, distal saccules were mildly dilated by chord length measurements. Epithelial differentiation as evaluated by immunohistochemical staining for markers of ciliated cells, Clara cells, alveolar type I cells and alveolar type II cells did not reveal a difference between Lamc2-/- and littermate control lungs. Likewise, vascular development, smooth muscle cell differentiation, and elastic fiber formation looked similar, as did airway basement membrane ultrastructure. Branching morphogenesis by lung bud culture was similar in Lamc2-/- and littermate control lungs. Since laminin-332 is important for hemidesmosome formation, we examined the structure of tracheal hemidesmosomes by transmission electron microscopy. Compared to littermate controls, Lamc2-/- tracheal hemidesmosomes were less organized and lacked the increased electron density associated with the basement membrane abutting the hemidesmosome.

Conclusion

These findings indicate that laminin γ2 and laminin-332, despite their prominence in the lung, have a minimal role in lung development through the saccular stage.

Epithelial laminin alpha5 is necessary for distal epithelial cell maturation, VEGF production, and alveolization in the developing murine lung

Laminin alpha5 is prominent in the basement membrane of alveolar walls, airways, and pleura in developing and adult lung. Targeted deletion of laminin alpha5 in mice causes developmental defects in multiple organs, but embryonic lethality has precluded examination of the latter stages of lung development. To identify roles for laminin alpha5 in lung development, we have generated an inducible lung epithelial cell-specific Lama5 null (SP-CLama5(fl/-)) mouse through use of the Cre/loxP system, the human surfactant protein C promoter, and the reverse tetracycline transactivator. SP-CLama5(fl/-) embryos exposed to doxycycline from E6.5 died a few hours after birth. Compared to control littermates, SP-CLama5(fl/-) lungs had dilated, enlarged distal airspaces, but basement membrane ultrastructure was preserved. Distal epithelial cell differentiation was perturbed, with a marked reduction of alveolar type II cells and a virtual absence of type I cells. Cell proliferation was reduced and apoptosis was increased. Capillary density was diminished, and this was associated with a decrease in total lung VEGF production. Overall, these findings indicate that epithelial laminin alpha5, independent of its structural function, is necessary for murine lung development, and suggest a role for laminin alpha5 in signaling pathways that promote alveolar epithelial cell differentiation and VEGF expression.

Placing Paleopolyploidy in Relation to Taxon Divergence: A Phylogenetic Analysis in Legumes Using 39 Gene Families

Young polyploid events are easily diagnosed by various methods, but older polyploid events become increasingly difficult to identify as chromosomal rearrangements, tandem gene or partial chromosome duplications, changes in substitution rates among duplicated genes, pseudogenization or locus loss, and interlocus interactions complicate the means of inferring past genetic events. Genomic data have provided valuable information about the polyploid history of numerous species, but on their own fail to show whether related species, each with a polyploid past, share a particular polyploid event. A phylogenetic approach provides a powerful method to determine this but many processes may mislead investigators. These processes can affect individual gene trees, but most likely will not affect all genes, and almost certainly will not affect all genes in the same way. Thus, a multigene approach, which combines the large-scale aspect of genomics with the resolution of phylogenetics, has the power to overcome these difficulties and allow us to infer genomic events further into the past than would otherwise be possible. Previous work using synonymous distances among gene pairs within species has shown evidence for large-scale duplications in the legumes Glycine max and Medicago truncatula. We present a case study using 39 gene families, each with three or four members in G. max and the putative orthologues in M. truncatula, rooted using Arabidopsis thaliana. We tested whether the gene duplications in these legumes occurred separately in each lineage after their divergence (Hypothesis 1), or whether they share a round of gene duplications (Hypothesis 2). Many more gene family topologies supported Hypothesis 2 over Hypothesis 1 (11 and 2, respectively), even after synonymous distance analysis revealed that some topologies were providing misleading results. Only ca. 33% of genes examined support either hypothesis, which strongly suggests that single gene family approaches may be insufficient when studying ancient events with nuclear DNA. Our results suggest that G. max and M. truncatula, along with approximately 7000 other legume species from the same clade, share an ancient round of gene duplications, either due to polyploidy or to some other process.

Cu(HCO2)2(pym) (pym = pyrimidine): Low-Dimensional Magnetic Behavior and Long-Range Ordering in a Quantum-Spin Lattice

We synthesized and structurally and magnetically characterized the novel 3D coordination polymer Cu(HCO2)2(pym) (pym = pyrimidine). The compound crystallizes in the monoclinic space group C2/c with a = 14.4639(8) A, b = 7.7209(4) A, c = 8.5172(5) A, beta = 126.076(2) degrees, and V= 768.76(7) A3. In the structure buckled layers of Cu(HCO2)2 are interconnected by pym ligands to afford 1D Cu-pym-Cu chains. Bulk magnetic susceptibility measurements show a broad maximum at 25 K that is indicative of short-range magnetic ordering. Between 12 and 300 K a least-squares fit of the chi(T) data to a mean-field-corrected antiferromagnetic chain model yielded excellent agreement for g = 2.224(3), J/kB = -26.9(2) K, and zJ'/kB = -1.1(3) K. Below approximately 3 K a transition to long-range magnetic ordering is observed, as suggested by a sharp and sudden decrease in chi(T). This result is corroborated by muon spin relaxation measurements that show oscillations in the muon asymmetry below T(N) = 2.802(1) K and rapidly fluctuating moments above T(N).

Mining EST databases to resolve evolutionary events in major crop species

Using plant EST collections, we obtained 1392 potential gene duplicates across 8 plant species: Zea mays, Oryza sativa, Sorghum bicolor, Hordeum vulgare, Solanum tuberosum, Lycopersicon esculentum, Medicago truncatula, and Glycine max. We estimated the synonymous and nonsynonymous distances between each gene pair and identified two to three mixtures of normal distributions corresponding to one to three rounds of genome duplication in each species. Within the Poaceae, we found a conserved duplication event among all four species that occurred approximately 50-60 million years ago (Mya); an event that probably occurred before the major radiation of the grasses. In the Solanaceae, we found evidence for a conserved duplication event approximately 50-52 Mya. A duplication in soybean occurred approximately 44 Mya and a duplication in Medicago about 58 Mya. Comparing synonymous and nonsynonymous distances allowed us to determine that most duplicate gene pairs are under purifying, negative selection. We calculated Pearson's correlation coefficients to provide us with a measure of how gene expression patterns have changed between duplicate pairs, and compared this across evolutionary distances. This analysis showed that some duplicates seemed to retain expression patterns between pairs, whereas others showed uncorrelated expression.

Reexamination of the Magnetic Properties of Cu2(dca)4(2,5-me2pyz) {dca = Dicyanamide; me2pyz = Dimethylpyrazine}: Isolated Spin-1/2 Dimers versus Long-Range Magnetic Ordering

The magnetic properties of Cu(2)(dca)(4)(2,5-me(2)pyz) have been reexamined. The extended structure of Cu(2)(dca)(4)(2,5-me(2)pyz) can be viewed in terms of Cu(2)(2,5-me(2)pyz)(4+) dimer units interconnected via mu(1,5)-dca ligands. The bulk magnetic susceptibility chi(T) and the isothermal M(H) of Cu(2)(dca)(4)(2,5-me(2)pyz) are shown to be well described by an isolated dimer model. This finding was confirmed by carrying out a spin dimer analysis based on tight-binding calculations, which shows that the 2,5-me(2)pyz ligand provides a substantial spin exchange interaction between the Cu(2+) ions while the dca ligands do not.

Soybean FGAM synthase promoters direct ectopic nematode feeding site activity

Soybean cyst nematode (SCN) resistance in soybean is a complex oligogenic trait. One of the most important nematode resistance genes, rhg1, has been mapped to a distal region of molecular linkage group G in soybean. A simplified genetic system to identify soybean genes with modified expression in response to SCN led to the identification of several genes within the nematode feeding sites. The genes were mapped to reveal their linkage relationship to known QTLs associated with soybean cyst nematode (SCN) resistance. One candidate, a phosphoribosyl formyl glycinamidine (FGAM) synthase (EC 6.3.5.3) gene, mapped to the same genomic interval as the major SCN resistance gene rhg1 within linkage group G. Isolation of FGAM synthase from a soybean bacterial artificial chromosome (BAC) library revealed two highly homologous paralogs. The genes appeared to be well conserved between bacteria and humans. Promoter analysis of the two soybean homologs was carried out with the Arabidopsis thaliana - Heterodera schachtii system to investigate gene response to nematode feeding. The two promoters and their derived deletion constructions effected green fluorescent protein (GFP) expression within nematode feeding sites. The 1.0-kb promoter sequence immediately adjacent to the translation start site was sufficient to direct expression of GFP within syncytia. A wound-inducible element and a floral organ expression sequence were also identified within these promoters. Although a nematode-responsive element could not be identified, the observed expression of GFP within feeding sites supports the hypothesis that plant gene expression is redirected within feeding sites to benefit the parasite.

Assignment of the Raman spectra of some deuterated-BEDT-TTF superconductors

We present the room-temperature Raman spectra of both the protonated and deuterated forms of kappa-(BEDT-TTF)2Cu[N(CN)2]Br, kappa-(BEDT-TTF)2Cu(NCS)2 and beta-(BEDT-TTF)2I3. Along with data for the neutral BEDT-TTF molecule these spectra are used to assign the many features in the spectra of the deuterated compounds.

Test for interlayer coherence in a quasi-two-dimensional superconductor

Peaks in the magnetoresistivity of the layered superconductor kappa - (BEDT-TTF)2Cu(NCS)(2), measured in fields < or =45 T applied within the layers, show that the Fermi surface is extended in the interlayer direction and enable the interlayer transfer integral (t( perpendicular) approximately 0.04 meV) to be deduced. However, the quasiparticle scattering rate tau(-1) is such that Planck's over 2pi/tau approximately 6t( perpendicular), implying that kappa - (BEDT-TTF)2Cu(NCS)(2) meets the criterion used to identify interlayer incoherence. The applicability of this criterion to anisotropic materials is thus shown to be questionable.

Thermal activation between Landau levels in the organic superconductor beta(")-(BEDT-TTF)2SF5CH2CF2SO3

We show that Shubnikov-de Haas oscillations in the interlayer resistivity of the organic superconductor beta(")-(BEDT-TTF)2SF5CH2CF2SO3 become very pronounced in magnetic fields approximately 60 T. The conductivity minima exhibit thermally activated behavior that can be explained simply by the presence of a Landau gap, with the quasi-one-dimensional Fermi surface sheets contributing negligibly to the conductivity. This observation, together with complete suppression of chemical potential oscillations, is consistent with an incommensurate nesting instability of the quasi-one-dimensional sheets.

Field-induced metal-insulator transition in a two-dimensional organic superconductor

The quasi-two-dimensional organic superconductor beta"-(BEDT-TTF)2SF5CH2CF2SO3 (Tc approximately 4.4 K) shows very strong Shubnikov-de Haas (SdH) oscillations which are superimposed on a highly anomalous steady background magnetoresistance, Rb. Comparison with de Haas-van Alphen oscillations allows a reliable estimate of Rb which is crucial for the correct extraction of the SdH signal. At low temperatures and high magnetic fields insulating behavior evolves. The magnetoresistance data violate Kohler's rule, i.e., cannot be described within the framework of semiclassical transport theory, but converge onto a universal curve appropriate for dynamical scaling at a metal-insulator transition.