Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize.

Transposable Elements (TEs) are mobile elements that contribute the majority of DNA sequences in the maize genome. Due to their repetitive nature, genomic studies of TEs are complicated by the difficulty of properly attributing multi-mapped short reads to specific genomic loci. Here, we utilize a method to attribute RNA-seq reads to TE families rather than particular loci in order to characterize transcript abundance for TE families in the maize genome. We applied this method to assess per-family expression of transposable elements in >800 published RNA-seq libraries representing a range of maize development, genotypes, and hybrids. While a relatively small proportion of TE families are transcribed, expression is highly dynamic with most families exhibiting tissue-specific expression. A large number of TE families were specifically detected in pollen and endosperm, consistent with reproductive dynamics that maintain silencing of TEs in the germ line. We find that B73 transcript abundance is a poor predictor of TE expression in other genotypes and that transcript levels can differ even for shared TEs. Finally, by assessing recombinant inbred line and hybrid transcriptomes, complex patterns of TE transcript abundance across genotypes emerged. Taken together, this study reveals a dynamic contribution of TEs to maize transcriptomes

Functional variants of DOG1 control seed chilling responses and variation in seasonal life-history strategies in Arabidopsis thaliana.

The seasonal timing of seed germination determines a plant's realized environmental niche, and is important for adaptation to climate. The timing of seasonal germination depends on patterns of seed dormancy release or induction by cold and interacts with flowering-time variation to construct different seasonal life histories. To characterize the genetic basis and climatic associations of natural variation in seed chilling responses and associated life-history syndromes, we selected 559 fully sequenced accessions of the model annual species Arabidopsis thaliana from across a wide climate range and scored each for seed germination across a range of 13 cold stratification treatments, as well as the timing of flowering and senescence. Germination strategies varied continuously along 2 major axes: 1) Overall germination fraction and 2) induction vs. release of dormancy by cold. Natural variation in seed responses to chilling was correlated with flowering time and senescence to create a range of seasonal life-history syndromes. Genome-wide association identified several loci associated with natural variation in seed chilling responses, including a known functional polymorphism in the self-binding domain of the candidate gene DOG1. A phylogeny of DOG1 haplotypes revealed ancient divergence of these functional variants associated with periods of Pleistocene climate change, and Gradient Forest analysis showed that allele turnover of candidate SNPs was significantly associated with climate gradients. These results provide evidence that A. thaliana's germination niche and correlated life-history syndromes are shaped by past climate cycles, as well as local adaptation to contemporary climate

Magnetic behavior of spin-chain compounds, Sr3ZnRhO6 and Ca3NiMnO6, from heat capacity and ac susceptibility studies

Heat-capacity (C) and ac susceptibility measurements have been performed on the spin-chain compounds, Sr3ZnRhO6 and Ca3NiMnO6, to establish their magnetic behavior and to explore whether there are magnetic frustration effects due to antiferromagnetic coupling of the chains arranged in a triangular fashion. While the paramagnetic Curie temperatures have been known to be large with a negative sign, as though antiferromagnetic interaction is very strong, the results establish that (i) the former apparently undergoes inhomogeneous magnetic ordering only around 15 K, however without spin-glass anomalies, and (ii) the latter orders antiferromagnetically at a relatively low temperature (17 K). Thus, the magnetic frustration manifests differently in these compounds.Comment: J. Solid State Chemistry, in pres

Using expression arrays for copy number detection: an example from E. coli.

BACKGROUND: The sequencing of many genomes and tiling arrays consisting of millions of DNA segments spanning entire genomes have made high-resolution copy number analysis possible. Microarray-based comparative genomic hybridization (array CGH) has enabled the high-resolution detection of DNA copy number aberrations. While many of the methods and algorithms developed for the analysis microarrays have focused on expression analysis, the same technology can be used to detect genetic alterations, using for example standard commercial Affymetrix arrays. Due to the nature of the resultant data, standard techniques for processing GeneChip expression experiments are inapplicable. RESULTS: We have developed a robust and flexible methodology for high-resolution analysis of DNA copy number of whole genomes, using Affymetrix high-density expression oligonucleotide microarrays. Copy number is obtained from fluorescence signals after processing with novel normalization, spatial artifact correction, data transformation and deletion/duplication detection. We applied our approach to identify deleted and amplified regions in E. coli mutants obtained after prolonged starvation. CONCLUSION: The availability of Affymetrix expression chips for a wide variety of organisms makes the proposed array CGH methodology useful more generally.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

Starch-gel investigations of the relationships between dehydrogenase proteins

A band which migrates, during starch-gel electrophoresis, to a far cathodal position, and catalyzes the reduction of nitro blue tetrazolium without the addition of substrate, has previously been found to also be associated with alcohol dehydrogenase (alcohol:NAD oxidoreductase, EC 1.1.1.1) and steroid activity. It is shown in the present report to be converted into an anodal glutamate dehydrogenase band (-glutamate: NAD (P) oxidoreductase (deaminating), EC 1.4.1.3) during storage of liver tissue. The intensity of the cathodal band increases when the concentration of the starch gel is increased, and is not seen after electrophoresis in agarose. Chemical examinations indicate that glutamate is present in the cathodal band. The liberation of glutamate dehydrogenase from the cathodal band is influenced by allosteric effectors. Conformational changes in the glutamate dehydrogenase, caused by these effectors, appear to correlate with the electrophoretic patterns obtained. Evidence is presented which suggests that the cathodal band can also liberate mitochondrial malate dehydrogenase bands (-malate:NAD oxidoreductase, EC 1.1.1.37). The possible significance of these results is discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/33286/1/0000678.pd

人工心臓への適用を目的としたダブルステータ型磁気浮上ポンプの開発

The clinical pharmacology of fentanyl and alfentanil was examined in opioid-experienced volunteers with agonist and antagonist sensitivity measures. Two studies used within-subject, placebo-controlled, crossover designs. In study 1, fentanyl (0.125, 0.25 mg/70 kg i.v.) was followed at 0, 20, 60 and 180 min by naloxone (10 mg/70 kg i.m.). Agonist effects during 180-min and 0-min (control; simultaneous fentanyl-naloxone i.v. infusion) challenge sessions were compared. Fentanyl rapidly constricted pupils, depressed respiration and produced subjective high and opiate symptoms lasting 60 to 120 min, depending on the measure. Naloxone precipitated withdrawal symptoms of comparable intensity at each challenge point. In study 2, fentanyl (0.125, 0.25 mg/70 kg i.v.), alfentanil (1, 2 mg/70 kg i.v.) and saline were followed at 1 and 6 hr by naloxone (10 mg/70 kg i.m.). Agonist effects were examined during 6-hr challenge sessions. The two drugs produced a comparable range of effects with similar peak magnitude for 0.125 mg/70 kg fentanyl and 1 mg/70 kg alfentanil and for 0.25 mg/70 kg fentanyl and 2 mg/70 kg alfentanil. Alfentanil\u27s duration of action was brief ( \u3c 60 min). Withdrawal was precipitated at 6 hr only after 0.25 mg/70 kg fentanyl. These findings support typical mu opioid characteristics (pleasurable subjective effects, physical dependence) for both drugs, differential duration of action (fentanyl \u3e alfentanil) and peak effects consistent with a 1:8 (fentanyl/alfentanil) potency ratio

Extended moment formation and magnetic ordering in the trigonal chain compound Ca3Co2O6

The results of electronic structure calculations for the one-dimensional magnetic chain compound Ca3Co2O6 are presented. The calculations are based on density functional theory and the local density approximation and used the augmented spherical wave (ASW) method. Our results allow for deeper understanding of recent experimental findings. In particular, alternation of Co 3d low- and high-spin states along the characteristic chains is related to differences in the oxygen coordination at the inequivalent cobalt sites. Strong hybridization of the d states with the O 2p states lays ground for polarization of the latter and the formation of extended localized magnetic moments centered at the high-spin sites. In contrast, strong metal-metal overlap along the chains gives rise to intrachain ferromagnetic exchange coupling of the extended moments via the d_{3z^2-r^2} orbitals of the low-spin cobalt atoms.Comment: 10 pages, 4 figures more information at http://www.physik.uni-augsburg.de/~eyert