Peculiar Bi-ion dynamics in Na1/2Bi1/2TiO3 from terahertz and microwave dielectric spectroscopy

Dynamics of the main dielectric anomaly in Na1/2Bi1/2TiO3 (NBT) was studied by time-domain THz and microwave spectroscopy, using also previously published data and their new overall fits. Above the dielectric maximum temperature Tm ~ 600 K, the response consists of coupled sub-THz oscillator and a relaxation mode, assigned to strongly anharmonic Bi-ion vibrations and hopping, whose slowing down explains the paraelectric-like permittivity increase to Tm. Below Tm, the main relaxation continues slowing down and additional relaxation, assigned to quasi-Debye losses, appears in the 10^11 Hz range. The oscillator hardens on cooling and takes over the whole oscillator strength. The permittivity decrease below Tm is caused by the reduced strength of the relaxations due to dominance of the rhombohedral phase within the coexistence region with the tetragonal phase. The anharmonic dynamics of Bi is supported by previous structural studies. NBT represents a hybrid between standard and relaxor ferroelectric behaviour

The transposable elements of the Drosophila melanogaster

Background: Transposable elements are found in the genomes of nearly all eukaryotes. The recent completion of the Release 3 euchromatic genomic sequence of Drosophila melanogaster by the Berkeley Drosophila Genome Project has provided precise sequence for the repetitive elements in the Drosophila euchromatin. We have used this genomic sequence to describe the euchromatic transposable elements in the sequenced strain of this species. Results: We identified 85 known and eight novel families of transposable element varying in copy number from one to 146. A total of 1,572 full and partial transposable elements were identified, comprising 3.86% of the sequence. More than two-thirds of the transposable elements are partial. The density of transposable elements increases an average of 4.7 times in the centromereproximal regions of each of the major chromosome arms. We found that transposable elements are preferentially found outside genes; only 436 of 1,572 transposable elements are contained within the 61.4 Mb of sequence that is annotated as being transcribed. A large proportion of transposable elements is found nested within other elements of the same or different classes. Lastly, an analysis of structural variation from different families reveals distinct patterns of deletion for elements belonging to different classes. Conclusions: This analysis represents an initial characterization of the transposable elements in the Release 3 euchromatic genomic sequence of D. melanogaster for which comparison to the transposable elements of other organisms can begin to be made. These data have been made available on the Berkeley Drosophila Genome Project website for future analyses

The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective.

BACKGROUND: Transposable elements are found in the genomes of nearly all eukaryotes. The recent completion of the Release 3 euchromatic genomic sequence of Drosophila melanogaster by the Berkeley Drosophila Genome Project has provided precise sequence for the repetitive elements in the Drosophila euchromatin. We have used this genomic sequence to describe the euchromatic transposable elements in the sequenced strain of this species. RESULTS: We identified 85 known and eight novel families of transposable element varying in copy number from one to 146. A total of 1,572 full and partial transposable elements were identified, comprising 3.86% of the sequence. More than two-thirds of the transposable elements are partial. The density of transposable elements increases an average of 4.7 times in the centromere-proximal regions of each of the major chromosome arms. We found that transposable elements are preferentially found outside genes; only 436 of 1,572 transposable elements are contained within the 61.4 Mb of sequence that is annotated as being transcribed. A large proportion of transposable elements is found nested within other elements of the same or different classes. Lastly, an analysis of structural variation from different families reveals distinct patterns of deletion for elements belonging to different classes. CONCLUSIONS: This analysis represents an initial characterization of the transposable elements in the Release 3 euchromatic genomic sequence of D. melanogaster for which comparison to the transposable elements of other organisms can begin to be made. These data have been made available on the Berkeley Drosophila Genome Project website for future analyses.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence

BACKGROUND: The Drosophila melanogaster genome was the first metazoan genome to have been sequenced by the whole-genome shotgun (WGS) method. Two issues relating to this achievement were widely debated in the genomics community: how correct is the sequence with respect to base-pair (bp) accuracy and frequency of assembly errors? And, how difficult is it to bring a WGS sequence to the accepted standard for finished sequence? We are now in a position to answer these questions. RESULTS: Our finishing process was designed to close gaps, improve sequence quality and validate the assembly. Sequence traces derived from the WGS and draft sequencing of individual bacterial artificial chromosomes (BACs) were assembled into BAC-sized segments. These segments were brought to high quality, and then joined to constitute the sequence of each chromosome arm. Overall assembly was verified by comparison to a physical map of fingerprinted BAC clones. In the current version of the 116.9 Mb euchromatic genome, called Release 3, the six euchromatic chromosome arms are represented by 13 scaffolds with a total of 37 sequence gaps. We compared Release 3 to Release 2; in autosomal regions of unique sequence, the error rate of Release 2 was one in 20,000 bp. CONCLUSIONS: The WGS strategy can efficiently produce a high-quality sequence of a metazoan genome while generating the reagents required for sequence finishing. However, the initial method of repeat assembly was flawed. The sequence we report here, Release 3, is a reliable resource for molecular genetic experimentation and computational analysis

A connectome and analysis of the adult Drosophila central brain.

The neural circuits responsible for animal behavior remain largely unknown. We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets. We define cell types, refine computational compartments, and provide an exhaustive atlas of cell examples and types, many of them novel. We provide detailed circuits consisting of neurons and their chemical synapses for most of the central brain. We make the data public and simplify access, reducing the effort needed to answer circuit questions, and provide procedures linking the neurons defined by our analysis with genetic reagents. Biologically, we examine distributions of connection strengths, neural motifs on different scales, electrical consequences of compartmentalization, and evidence that maximizing packing density is an important criterion in the evolution of the fly's brain

The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective.

BACKGROUND: Transposable elements are found in the genomes of nearly all eukaryotes. The recent completion of the Release 3 euchromatic genomic sequence of Drosophila melanogaster by the Berkeley Drosophila Genome Project has provided precise sequence for the repetitive elements in the Drosophila euchromatin. We have used this genomic sequence to describe the euchromatic transposable elements in the sequenced strain of this species. RESULTS: We identified 85 known and eight novel families of transposable element varying in copy number from one to 146. A total of 1,572 full and partial transposable elements were identified, comprising 3.86% of the sequence. More than two-thirds of the transposable elements are partial. The density of transposable elements increases an average of 4.7 times in the centromere-proximal regions of each of the major chromosome arms. We found that transposable elements are preferentially found outside genes; only 436 of 1,572 transposable elements are contained within the 61.4 Mb of sequence that is annotated as being transcribed. A large proportion of transposable elements is found nested within other elements of the same or different classes. Lastly, an analysis of structural variation from different families reveals distinct patterns of deletion for elements belonging to different classes. CONCLUSIONS: This analysis represents an initial characterization of the transposable elements in the Release 3 euchromatic genomic sequence of D. melanogaster for which comparison to the transposable elements of other organisms can begin to be made. These data have been made available on the Berkeley Drosophila Genome Project website for future analyses.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Peculiar Bi-ion dynamics in Na1/2Bi1/2TiO3from terahertz and microwave dielectric spectroscopy

Dynamics of the main dielectric anomaly in Na1/2Bi1/2TiO3 (NBT) were studied by time-domain THz and microwave spectroscopy, using also previously published data and their new overall fits. Above the dielectric maximum temperature Tm ≈ 600 K, the response consists of coupled sub-THz oscillator and a relaxation mode, assigned to strongly anharmonic Bi-ion vibrations and hopping, whose slowing down explains the paraelectric-like permittivity increase to Tm. Below Tm, the main relaxation continues slowing down and additional relaxation, assigned to quasi-Debye losses, appears in the 1011 Hz range. The oscillator hardens on cooling and takes over the whole oscillator strength. The permittivity decrease below Tm is caused by the reduced strength of the relaxations due to dominance of the rhombohedral phase within the coexistence region with the tetragonal phase. The anharmonic dynamics of Bi are supported by previous structural studies. NBT represents a hybrid between standard and relaxor ferroelectric behaviour

High-Throughput Plasmid cDNA Library Screening

Libraries of cDNA clones are valuable resources for analysing the expression, structure, and regulation of genes, as well as for studying protein functions and interactions. Full-length cDNA clones provide information about intron and exon structures, splice junctions and 5'- and 3'-untranslated regions (UTRs). Open reading frames (ORFs) derived from cDNA clones can be used to generate constructs allowing expression of native proteins and N- or C-terminally tagged proteins. Thus, obtaining full-length cDNA clones and sequences for most or all genes in an organism is critical for understanding genome functions. Expressed sequence tag (EST) sequencing samples cDNA libraries at random, which is most useful at the beginning of large-scale screening projects. However, as projects progress towards completion, the probability of identifying unique cDNAs via EST sequencing diminishes, resulting in poor recovery of rare transcripts. We describe an adapted, high-throughput protocol intended for recovery of specific, full-length clones from plasmid cDNA libraries in five days

High-Throughput Plasmid cDNA Library Screening

Libraries of cDNA clones are valuable resources for analysing the expression, structure, and regulation of genes, as well as for studying protein functions and interactions. Full-length cDNA clones provide information about intron and exon structures, splice junctions and 5'- and 3'-untranslated regions (UTRs). Open reading frames (ORFs) derived from cDNA clones can be used to generate constructs allowing expression of native proteins and N- or C-terminally tagged proteins. Thus, obtaining full-length cDNA clones and sequences for most or all genes in an organism is critical for understanding genome functions. Expressed sequence tag (EST) sequencing samples cDNA libraries at random, which is most useful at the beginning of large-scale screening projects. However, as projects progress towards completion, the probability of identifying unique cDNAs via EST sequencing diminishes, resulting in poor recovery of rare transcripts. We describe an adapted, high-throughput protocol intended for recovery of specific, full-length clones from plasmid cDNA libraries in five days

Mixology of MA1-xEAxPbI3 Hybrid Perovskites: Phase Transitions, Cation Dynamics and Photoluminescence

Mixing of molecular cations in hybrid lead halide perovskites is a highly effective approach to enhance stability and performance of the optoelectronic devices based on these compounds. In this work, we prepare and study novel mixed methylammonium (MA)-ethylammonium (EA) MA1-xEAxPbI3 (x < 0.4) hybrid perovskites. We use a suite of different techniques to determine the structural phase diagram, cation dynamics and photoluminescence properties of these compounds. Upon introduction of EA, we observe a gradual lowering of the phase transition temperatures indicating stabilization of the cubic phase. For mixing levels higher than 30%, we obtain a complete suppression of the low-temperature phase transition and formation of a new tetragonal phase with different symmetry. We use the broadband dielectric spectroscopy to study the dielectric response of the mixed compounds in an extensive frequency range, which allows us to distinguish and characterize three distinct dipolar relaxation processes related to the molecular cation dynamics. We observe that mixing increases the rotation barrier of the MA cations and tunes the dielectric permittivity values. For the highest mixing levels, we observe signatures of the dipolar glass phase formation. Our findings are supported by the density functional theory calculations. Our photoluminescence measurements reveal a small change of the band gap upon mixing indicating suitability of these compounds for optoelectronic applications