Formation of small-scale irregularities in the auroral E region

In this thesis, knowledge on the production mechanisms of small scale (meter and decameter) irregularities in the auroral E region is advanced, both theoretically and experimentally. In the theoretical part of the thesis, the linear fluid theory of the Farley-Buneman (F-B) and gradient drift (G-D) plasma instabilities is considered. A general 2-D dispersion equation is derived and analyzed. Then, a review of existing nonlinear theories is given. The thrust is on the theory predictions with respect to the phase velocity of plasma waves. As an expansion of the theory, one new effect in the F-B instability evolution is considered, a secondary instability of a turbulent background of the primary F-B waves. It is shown that in a system of F-B modes the energy can flow from the short-wavelength (primary) to long-wavelength (secondary) struc­tures (inverse cascade), contrary to the currently dominating idea that the energy of unstable waves is transferred to the smaller-scale structures. The phase velocity of the secondary waves propagating along the electron flow was found to be close to the electron streaming velocity and not saturated at the ion acoustic speed of the plasma. A possibility of decameter wave generation through this mechanism is envisioned. Experimentally, data of 2 separate experiments carried out in the auroral E region to study phase velocity of meter and decameter irregularities are considered. First, nearly simultaneous measurements of two Super Dual Auroral Radar Network (Super­DARN) HF radars (12 MHz, scatter from decameter waves, λ = 12 m) and one VHF radar (50 MHz, scatter from meter waves, λ = 3 m) at the Antarctic Syowa station are compared. It is demonstrated that HF echoes exhibit quite different characteristics as compared to VHF echoes so that HF echoes with low ( 350 m s-1) Doppler velocities are proposed to consider separately. Observations indicate that the high-velocity HF echoes exhibit properties similar to VHF echoes while the low-velocity HF echoes do not have a VHF counterpart. Other echo characteristics are also studied. For example, the preferential direction for the HF echo occurrence was found to be shifted by 45° from the direction of the electron flow and this shift was related to the existence of the low-velocity echoes in the data statistics. In the second experiment, the characteristics of decameter irregularities at 5 very close scales (between 10 and 16 m) are investigated by considering SuperDARN observations at Prince George, British Columbia, Canada. It is shown that the measured Doppler velocity (and hence the phase velocity of plasma waves) depends on the irregularity scale but only for irregularities propagating within the F-B instability cone. For these directions, the phase velocity was also found to decrease with the aspect angle and the rate of the decrease was found to be scale sensitive. Very little velocity variation with the aspect angle was discovered for observations outside of the F-B instability cone. Several factors potentially contributing to the observed HF and VHF echo characteristics in both experiments are identified and discussed. These are the geophysical conditions during measurements (details of large-scale convection patterns, a possibility of scatter from meteor trails), propagation effects (focusing of the HF radio waves onto various parts of the electrojet layer) and the plasma physics of irregularity formation (effects of strong gradients of the background electron density, ion and neutral particle motions, mode coupling, anomalous collisions). It is argued that the high-velocity HF echoes and VHF echoes are generated through traditional F-B and G-D instabilities, while the low-velocity HF echoes can have additional sources. Finally, several suggestions for further research are presented

Profiling expression changes caused by a segmental aneuploid in maize

<p>Abstract</p> <p>Background</p> <p>While changes in chromosome number that result in aneuploidy are associated with phenotypic consequences such as Down syndrome and cancer, the molecular causes of specific phenotypes and genome-wide expression changes that occur in aneuploids are still being elucidated.</p> <p>Results</p> <p>We employed a segmental aneuploid condition in maize to study phenotypic and gene expression changes associated with aneuploidy. Maize plants that are trisomic for 90% of the short arm of chromosome 5 and monosomic for a small distal portion of the short arm of chromosome 6 exhibited a phenotypic syndrome that includes reduced stature, tassel morphology changes and the presence of knots on the leaves. The knotted-like homeobox gene <it>knox10</it>, which is located on the short arm of chromosome 5, was shown to be ectopically expressed in developing leaves of the aneuploid plants. Expression profiling revealed that ~40% of the expressed genes in the trisomic region exhibited the expected 1.5 fold increased transcript levels while the remaining 60% of genes did not show altered expression even with increased gene dosage.</p> <p>Conclusion</p> <p>We found that the majority of genes with altered expression levels were located within the chromosomal regions affected by the segmental aneuploidy and exhibits dosage-dependent expression changes. A small number of genes exhibit higher levels of expression change not predicted by the dosage, or display altered expression even though they are not located in the aneuploid regions.</p

Comparison of flow angle variations of E-region echo characteristics at VHF and HF

In this study, characteristics of the auroral E-region echoes at two significantly different radar frequencies of 12 and 50 MHz are compared. Considered observations were performed at the Syowa Antarctic station in March of 1997 using two HF and one VHF radars at various angles with respect to the magnetic L shells. The diurnal variation of echo occurrence was found to be similar at two frequencies and consistent with previous studies. On the other hand, variation of echo occurrence with L-shell angle φ was shown to be significantly different at two frequencies. 50-MHz echoes were detected preferentially along the L shell (dominating direction of the electrojet flow) while 12-MHz echoes were detected in a broad range of azimuths with the maximum in echo occurrence at φ=40-50°. By plotting the Doppler velocity versus L-shell angle, we demonstrate that 12-MHz echoes can be divided into two populations, the high- and low-velocity echoes. The high-velocity echoes were observed mostly along the L shells while the low-velocity echoes were observed at all directions. We also show that the echo populations exhibit different variation of the Doppler velocity with the L-shell angle. We argue that while the 50-MHz echoes are related to the Farley-Buneman and gradient drift plasma instabilities, the 12-MHz echoes can have additional sources, such as the thermo-diffusion instability and/or neutral wind-related plasma instabilities

Transposable elements contribute to activation of maize genes in response to abiotic stress. PLoS Genet

Abstract Transposable elements (TEs) account for a large portion of the genome in many eukaryotic species. Despite their reputation as &apos;&apos;junk&apos;&apos; DNA or genomic parasites deleterious for the host, TEs have complex interactions with host genes and the potential to contribute to regulatory variation in gene expression. It has been hypothesized that TEs and genes they insert near may be transcriptionally activated in response to stress conditions. The maize genome, with many different types of TEs interspersed with genes, provides an ideal system to study the genome-wide influence of TEs on gene regulation. To analyze the magnitude of the TE effect on gene expression response to environmental changes, we profiled gene and TE transcript levels in maize seedlings exposed to a number of abiotic stresses. Many genes exhibit up-or down-regulation in response to these stress conditions. The analysis of TE families inserted within upstream regions of up-regulated genes revealed that between four and nine different TE families are associated with up-regulated gene expression in each of these stress conditions, affecting up to 20% of the genes up-regulated in response to abiotic stress, and as many as 33% of genes that are only expressed in response to stress. Expression of many of these same TE families also responds to the same stress conditions. The analysis of the stress-induced transcripts and proximity of the transposon to the gene suggests that these TEs may provide local enhancer activities that stimulate stress-responsive gene expression. Our data on allelic variation for insertions of several of these TEs show strong correlation between the presence of TE insertions and stress-responsive upregulation of gene expression. Our findings suggest that TEs provide an important source of allelic regulatory variation in gene response to abiotic stress in maize

Genome size diversity in angiosperms and its influence on gene space

Genome size varies c. 2400-fold in angiosperms (flowering plants), although the range of genome size is skewed towards small genomes, with a mean genome size of 1C = 5.7 Gb. One of the most crucial factors governing genome size in angiosperms is the relative amount and activity of repetitive elements. Recently, there have been new insights into how these repeats, previously discarded as ‘junk’ DNA, can have a significant impact on gene space (i.e. the part of the genome comprising all the genes and gene-related DNA). Here we review these new findings and explore in what ways genome size itself plays a role in influencing how repeats impact genome dynamics and gene space, including gene expression

Genomic Responses to Abnormal Gene Dosage: The X Chromosome Improved on a Common Strategy

This new primer, which discusses a study by Zhang et al., provides an overview of the process by which chromosomes achieve dose compensation and the mechanisms underlying this phenomenon in Drosophila S2 cells

Widespread Occurrence of Dosage Compensation in Candida albicans

The important human pathogen Candida albicans possesses an unusual form of gene regulation, in which the copy number of an entire specific chromosome or a large portion of a specific chromosome changes in response to a specific adverse environment, thus, insuring survival. In the absence of the adverse environment, the altered portion of the genome can be restored to its normal condition. One major question is how C. albicans copes with gene imbalance arising by transitory aneuploid states. Here, we compared transcriptomes from cells with either two copies or one copy of chromosome 5 (Ch5) in, respectively, a diploid strain 3153A and its representative derivative Sor55. Statistical analyses revealed that at least 40% of transcripts from the monosomic Ch5 are fully compensated to a disomic level, thus, indicating the existence of a genome-wide mechanism maintaining cellular homeostasis. Only approximately 15% of transcripts were diminished twofold in accordance with what would be expected for Ch5 monosomy. Another minor portion of approximately 6% of transcripts, unexpectedly, increased up to twofold and higher than the disomic level, demonstrating indirect control by monosomy. Array comparative genome hybridization revealed that only few out of approximately 500 genes on the monosomic Ch5b were duplicated, thus, not causing a global up regulation. Dosage compensation was confirmed with several representative genes from another monosomic Ch5a in the mutant Sor60. We suggest that C. albicans's unusual regulation of gene expression by the loss and gain of entire chromosomes is coupled with widespread compensation of gene dosage at the transcriptional level

Brd1 Gene in Maize Encodes a Brassinosteroid C-6 Oxidase

The role of brassinosteroids in plant growth and development has been well-characterized in a number of plant species. However, very little is known about the role of brassinosteroids in maize. Map-based cloning of a severe dwarf mutant in maize revealed a nonsense mutation in an ortholog of a brassinosteroid C-6 oxidase, termed brd1, the gene encoding the enzyme that catalyzes the final steps of brassinosteroid synthesis. Homozygous brd1–m1 maize plants have essentially no internode elongation and exhibit no etiolation response when germinated in the dark. These phenotypes could be rescued by exogenous application of brassinolide, confirming the molecular defect in the maize brd1-m1 mutant. The brd1-m1 mutant plants also display alterations in leaf and floral morphology. The meristem is not altered in size but there is evidence for differences in the cellular structure of several tissues. The isolation of a maize mutant defective in brassinosteroid synthesis will provide opportunities for the analysis of the role of brassinosteroids in this important crop system

Buffering of Segmental and Chromosomal Aneuploidies in Drosophila melanogaster

Chromosomal instability, which involves the deletion and duplication of chromosomes or chromosome parts, is a common feature of cancers, and deficiency screens are commonly used to detect genes involved in various biological pathways. However, despite their importance, the effects of deficiencies, duplications, and chromosome losses on the regulation of whole chromosomes and large chromosome domains are largely unknown. Therefore, to explore these effects, we examined expression patterns of genes in several Drosophila deficiency hemizygotes and a duplication hemizygote using microarrays. The results indicate that genes expressed in deficiency hemizygotes are significantly buffered, and that the buffering effect is general rather than being mainly mediated by feedback regulation of individual genes. In addition, differentially expressed genes in haploid condition appear to be generally more strongly buffered than ubiquitously expressed genes in haploid condition, but, among genes present in triploid condition, ubiquitously expressed genes are generally more strongly buffered than differentially expressed genes. Furthermore, we show that the 4th chromosome is compensated in response to dose differences. Our results suggest general mechanisms have evolved that stimulate or repress gene expression of aneuploid regions as appropriate, and on the 4th chromosome of Drosophila this compensation is mediated by Painting of Fourth (POF)