Pollen-Specific Activation of Arabidopsis Retrogenes Is Associated with Global Transcriptional Reprogramming

Duplications allow for gene functional diversification and accelerate genome evolution. Occasionally, the transposon amplification machinery reverse transcribes the mRNA of a gene, integrates it into the genome, and forms an RNA-duplicated copy: the retrogene. Although retrogenes have been found in plants, their biology and evolution are poorly understood. Here, we identified 251 (216 novel) retrogenes in Arabidopsis thaliana, corresponding to 1% of protein-coding genes. Arabidopsis retrogenes are derived from ubiquitously transcribed parents and reside in gene-rich chromosomal regions. Approximately 25% of retrogenes are cotranscribed with their parents and 3% with head-to-head oriented neighbors. This suggests transcription by novel promoters for 72% of Arabidopsis retrogenes. Many retrogenes reach their transcription maximum in pollen, the tissue analogous to animal spermatocytes, where upregulation of retrogenes has been found previously. This implies an evolutionarily conserved mechanism leading to this transcription pattern of RNA-duplicated genes. During transcriptional repression, retrogenes are depleted of permissive chromatin marks without an obvious enrichment for repressive modifications. However, this pattern is common to many other pollen-transcribed genes independent of their evolutionary origin. Hence, retroposition plays a role in plant genome evolution, and the developmental transcription pattern of retrogenes suggests an analogous regulation of RNA-duplicated genes in plants and animals

Answer to Wang and Luo, "Polyploidization increases meiotic recombination frequency in Arabidopsis: a close look at statistical modelling and data analysis"

This article is a response to Wang and Luo

Insights into the role of transcriptional gene silencing in response to herbicide-Treatments in Arabidopsis thaliana

Herbicide resistance is broadly recognized as the adaptive evolution of weed populations to the intense selection pressure imposed by the herbicide applications. Here, we tested whether tran- scriptional gene silencing (TGS) and RNA-directed DNA Methylation (RdDM) pathways modulate resistance to commonly applied herbicides. Using Arabidopsis thaliana wild-type plants exposed to sublethal doses of glyphosate, imazethapyr, and 2,4-D, we found a partial loss of TGS and increased susceptibility to herbicides in six out of 11 tested TGS/RdDM mutants. Mutation in REPRESSOR OF SILENCING 1 (ROS1), that plays an important role in DNA demethylation, leading to strongly in- creased susceptibility to all applied herbicides, and imazethapyr in particular. Transcriptomic analysis of the imazethapyr-treated wild type and ros1 plants revealed a relation of the herbicide upregu- lated genes to chemical stimulus, secondary metabolism, stress condition, flavonoid biosynthesis, and epigenetic processes. Hypersensitivity to imazethapyr of the flavonoid biosynthesis component TRANSPARENT TESTA 4 (TT4) mutant plants strongly suggests that ROS1-dependent accumulation of flavonoids is an important mechanism for herbicide stress response in A. thaliana. In summary, our study shows that herbicide treatment affects transcriptional gene silencing pathways and that misregulation of these pathways makes Arabidopsis plants more sensitive to herbicide treatment

Influence of fouling on compressor dynamics: Experimental and modelling approach

The effect of compressor fouling on the performance of a gas turbine has been the subject of several papers; however, the goal of this paper is to address a more fundamental question of the effect of fouling, which is the onset of unstable operation of the compressor. Compressor fouling experiments have been carried out on a test rig refitted with TJ100 small jet engine with centrifugal compressor. Fouling on the compressor blade was simulated with texturized paint with average roughness value of 6 microns. Compressor characteristic was measured for both the clean (baseline) and fouled compressor blades at several rotational speeds by throttling the engine with variable exhaust nozzle. A Greitzer-type compression system model has been applied based on the geometric and performance parameters of the TJ100 small jet engine test rig. Frequency of plenum pressure fluctuation, the mean disturbance flow coefficient and pressure-rise coefficient at the onset of plenum flowfield disturbance predicted by the model was compared with the measurement for both the baseline and fouled engine. Model prediction of the flowfield parameters at inception of unstable operation in the compressor showed good agreement with the experimental data. The results proved that used simple Greitzer model is suitable for prediction of the engine compressor unstable behaviour and prediction of the mild surge inception point for both the clean and the fouled compressor

In service inspections of thick walled concrete sructures

Ageing management and renewal of the operating license of existing NPP’s are at present the main problems of nuclear power industry. For the ageing management of concrete structures the OECD-Nuclear Energy Agency, Committee on the Safety on Nuclear Installations defined as the first priority ISI techniques for reinforced concrete structures having thick sections and areas not directly accessible for inspections. We discuss the NRI Rez research and development program in this field, as well as results, which will be used for qualification of the ISI techniques.Основними проблемами ядерної енергетики є контроль за процесом старін­ня і відновлення операційних ліцензій існуючих атомних станцій. В якості найбільш пріоритетного направлення контролю за процесом старіння бетон­них конструкцій використовуються так зван ISI-методи для залізобетонних товстостінних онструкцій,що мають недоступні для огляду місця.Обгово­рюється науково-дослідна програма в цій області,а також деякі результати, що використовуються в кваліфікаційному аналізі ISI-методів.Основными проблемами ядерной энергетики являются контроль процесса старения и возобновление операционных лицензий существующих атомных станций. В качестве наиболее приоритетного направления контроля процесса старения бетонных конструкций используются так называемые lSl-методы для железобетонных толстостенных конструкций с недоступными для осмотра участками. Обсуждается научно-исследовательская программа в этой области, а также некоторые результаты, используемые в квалификационном анализе lSl-методов

Tandem repetitive transgenes and fluorescent chromatin tags alter local interphase chromosome arrangement in Arabidopsis thaliana

Fluorescent protein chromatin tagging as achieved by the lac operator/lac repressor system is useful to trace distinct chromatin domains in living eukaryotic nuclei. To interpret the data correctly, it is important to recognize influences of the tagging system on nuclear architecture of the host cells. Within an Arabidopsis line that carries lac operator/lac repressor/GFP transgenes, the transgene loci frequently associate with each other and with heterochromatic chromocenters. Accumulation of tagged fusion protein further enhances the association frequency. Independent experiments with a transgenic plant carrying another multi-copy transgene also revealed, independent of its transcriptional state, unusually high frequencies of association with each other and with heterochromatin. From these results we conclude that the lac operator/lac repressor chromatin tagging system may alter the spatial chromatin organization in the host nuclei (in particular when more than one insertion locus is present) and also that loci of homologous transgenic repeats associate more often with each other and with endogenous heterochromatin than normal euchromatic regions

Polyploidization increases meiotic recombination frequency in Arabidopsis

<p>Abstract</p> <p>Background</p> <p>Polyploidization is the multiplication of the whole chromosome complement and has occurred frequently in vascular plants. Maintenance of stable polyploid state over generations requires special mechanisms to control pairing and distribution of more than two homologous chromosomes during meiosis. Since a minimal number of crossover events is essential for correct chromosome segregation, we investigated whether polyploidy has an influence on the frequency of meiotic recombination.</p> <p>Results</p> <p>Using two genetically linked transgenes providing seed-specific fluorescence, we compared a high number of progeny from diploid and tetraploid <it>Arabidopsis </it>plants. We show that rates of meiotic recombination in reciprocal crosses of genetically identical diploid and autotetraploid <it>Arabidopsis </it>plants were significantly higher in tetraploids compared to diploids. Although male and female gametogenesis differ substantially in meiotic recombination frequency, both rates were equally increased in tetraploids. To investigate whether multivalent formation in autotetraploids was responsible for the increased recombination rates, we also performed corresponding experiments with allotetraploid plants showing strict bivalent pairing. We found similarly increased rates in auto- and allotetraploids, suggesting that the ploidy effect is independent of chromosome pairing configurations.</p> <p>Conclusions</p> <p>The evolutionary success of polyploid plants in nature and under domestication has been attributed to buffering of mutations and sub- and neo-functionalization of duplicated genes. Should the data described here be representative for polyploid plants, enhanced meiotic recombination, and the resulting rapid creation of genetic diversity, could have also contributed to their prevalence.</p

Response to Wang and Luo

This article is a response to Wang and Luo