Landscape of gene transposition-duplication within the Brassicaceae family

© The Author(s) 2018. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. We developed the CLfinder-OrthNet pipeline that detects co-linearity among multiple closely related genomes, finds orthologous gene groups, and encodes the evolutionary history of each orthologue group into a representative network (OrthNet). Using a search based on network topology, we identified 1,394 OrthNets that included gene transposition-duplication (tr-d) events, out of 17,432 identified in six Brassicaceae genomes. Occurrences of tr-d shared by subsets of Brassicaceae genomes mirrored the divergence times between the genomes and their repeat contents. The majority of tr-d events resulted in truncated open reading frames (ORFs) in the duplicated loci. However, the duplicates with complete ORFs were significantly more frequent than expected from random events. These were derived from older tr-d events and had a higher chance of being expressed. We also found an enrichment of tr-d events with complete loss of intergenic sequence conservation between the original and duplicated loci. Finally, we identified tr-d events uniquely found in two extremophytes among the six Brassicaceae genomes, including tr-d of SALT TOLERANCE 32 and ZINC TRANSPORTER 3 that relate to their adaptive evolution. CLfinder-OrthNet provides a flexible toolkit to compare gene order, visualize evolutionary paths among orthologues as networks, and identify gene loci that share an evolutionary history

GOMCL: a t GOMCL: a toolkit t oolkit to cluster o cluster, evaluate, and extr aluate, and extract non-r act non-redundant edundant associations of Gene Ontology-based functions

Background Functional enrichment of genes and pathways based on Gene Ontology (GO) has been widely used to describe the results of various -omics analyses. GO terms statistically overrepresented within a set of a large number of genes are typically used to describe the main functional attributes of the gene set. However, these lists of overrepresented GO terms are often too large and contains redundant overlapping GO terms hindering informative functional interpretations. Results We developed GOMCL to reduce redundancy and summarize lists of GO terms effectively and informatively. This lightweight python toolkit efficiently identifies clusters within a list of GO terms using the Markov Clustering (MCL) algorithm, based on the overlap of gene members between GO terms. GOMCL facilitates biological interpretation of a large number of GO terms by condensing them into GO clusters representing non-overlapping functional themes. It enables visualizing GO clusters as a heatmap, networks based on either overlap of members or hierarchy among GO terms, and tables with depth and cluster information for each GO term. Each GO cluster generated by GOMCL can be evaluated and further divided into non-overlapping sub-clusters using the GOMCL-sub module. The outputs from both GOMCL and GOMCL-sub can be imported to Cytoscape for additional visualization effects. Conclusions GOMCL is a convenient toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. GOMCL helps researchers to reduce time spent on manual curation of large lists of GO terms, minimize biases introduced by redundant GO terms in data interpretation, and batch processing of multiple GO enrichment datasets. A user guide, a test dataset, and the source code of GOMCL are available at and

Locomotion Control of a Compliant Legged Robot from Slow Walking to Fast Running Regular Paper

In this paper, we propose a locomotion control method for a compliant legged robot from slow walking to fast running. We also examine the energy efficiency of the compliant legged robot controlled by the proposed locomotion control method. Experimentally, we obtain the robot running speed of about 4.3m/s with the initial compliant leg length of 0.1m. In addition, we obtain very good energy efficiency. In the best case, the mechanical cost of transport(Cmt), known as an energy efficiency measure, is obtained at about 0.2. Comparing with the other energy efficient robots, our robot exhibits very good energy efficiency. © 2012 Kim et al.; licensee InTech.1

Life at the extreme: Lessons from the genome

© 2012 BioMed Central Ltd. Extremophile plants thrive in places where most plant species cannot survive. Recent developments in high-throughput technologies and comparative genomics are shedding light on the evolutionary mechanisms leading to their adaptation

H2 pressure swing adsorption for IGCC power plant and techno-economic analysis of integrating PSA to IGCC with carbon capture

Carbon capture and sequestration technologies emerge as the effectual remediation processes to reduce CO2 emissions from coal power plants. Integrated gasification combined cycle (IGCC) is a representative technology for utilizing coal as feedstock and is consequently playing a more important role to cover the global energy demand. The IGCC produces H2-rich mixture at high pressures (30-35 bar) after capturing CO2. It is reported that the high purity H2 recovered from the IGCC process can be economically supplied to a hydrogen turbine or fuel cell. And a PSA process is a strong candidate to produce high purity H2 from the IGCC effluent gas. However, due to higher operating pressure than the present H2 PSA processes, reducing the operating costs and efficiency has emerged as one of the key issues. Please click Additional Files below to see the full abstract

4C-seq characterization of Drosophila BEAF binding regions provides evidence for highly variable long-distance interactions between active chromatin

© 2018 Shrestha et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Chromatin organization is crucial for nuclear functions such as gene regulation, DNA replication and DNA repair. Insulator binding proteins, such as the Drosophila Boundary Element-Associated Factor (BEAF), are involved in chromatin organization. To further understand the role of BEAF, we detected cis-and trans-interaction partners of four BEAF binding regions (viewpoints) using 4C (circular chromosome conformation capture) and analyzed their association with different genomic features. Previous genome-wide mapping found that BEAF usually binds near transcription start sites, often of housekeeping genes, so our viewpoints were selected to reflect this. Our 4C data show the interaction partners of our viewpoints are highly variable and generally enriched for active chromatin marks. The most consistent association was with housekeeping genes, a feature in common with our viewpoints. Fluorescence in situ hybridization indicated that the long-distance interactions occur even in the absence of BEAF. These data are most consistent with a model in which BEAF is redundant with other factors found at active promoters. Our results point to principles of long-distance interactions made by active chromatin, supporting a previously proposed model in which condensed chromatin is sticky and associates into topologically associating domains (TADs) separated by active chromatin. We propose that the highly variable long-distance interactions we detect are driven by redundant factors that open chromatin to promote transcription, combined with active chromatin filling spaces between TADs while packing of TADs relative to each other varies from cell to cell

Low-Phosphate Chromatin Dynamics Predict a Cell Wall Remodeling Network in Rice Shoots

© 2020 American Society of Plant Biologists. All Rights Reserved. Phosphorus (P) is an essential plant macronutrient vital to fundamental metabolic processes. Plant-available P is low in most soils, making it a frequent limiter of growth. Declining P reserves for fertilizer production exacerbates this agricultural challenge. Plants modulate complex responses to fluctuating P levels via global transcriptional regulatory networks. Although chromatin structure plays a substantial role in controlling gene expression, the chromatin dynamics involved in regulating P homeostasis have not been determined. Here we define distinct chromatin states across the rice (Oryza sativa) genome by integrating multiple chromatin marks, including the H2A.Z histone variant, H3K4me3 modification, and nucleosome positioning. In response to P starvation, 40% of all protein-coding genes exhibit a transition from one chromatin state to another at their transcription start site. Several of these transitions are enriched in subsets of genes differentially expressed under P deficiency. The most prominent subset supports the presence of a coordinated signaling network that targets cell wall structure and is regulated in part via a decrease of H3K4me3 at transcription start sites. The P starvation-induced chromatin dynamics and correlated genes identified here will aid in enhancing P use efficiency in crop plants, benefitting global agriculture

Compromised RNA polymerase III complex assembly leads to local alterations of intergenic RNA polymerase II transcription in Saccharomyces cerevisiae

© 2014 Wang et al. Background: Assembled RNA polymerase III (Pol III) complexes exert local effects on chromatin processes, including influencing transcription of neighboring RNA polymerase II (Pol II) transcribed genes. These properties have been designated as \u27extra-transcriptional\u27 effects of the Pol III complex. Previous coding sequence microarray studies using Pol III factor mutants to determine global effects of Pol III complex assembly on Pol II promoter activity revealed only modest effects that did not correlate with the proximity of Pol III complex binding sites. Results: Given our recent results demonstrating that tDNAs block progression of intergenic Pol II transcription, we hypothesized that extra-transcriptional effects within intergenic regions were not identified in the microarray study. To reconsider global impacts of Pol III complex binding, we used RNA sequencing to compare transcriptomes of wild type versus Pol III transcription factor TFIIIC depleted mutants. The results reveal altered intergenic Pol II transcription near TFIIIC binding sites in the mutant strains, where we observe readthrough of upstream transcripts that normally terminate near these sites, 5\u27- and 3\u27-extended transcripts, and de-repression of adjacent genes and intergenic regions. Conclusions: The results suggest that effects of assembled Pol III complexes on transcription of neighboring Pol II promoters are of greater magnitude than previously appreciated, that such effects influence expression of adjacent genes at transcriptional start site and translational levels, and may explain a function of the conserved ETC sites in yeast. The results may also be relevant to synthetic biology efforts to design a minimal yeast genome

Intracellular consequences of SOS1 deficiency during salt stress

A mutation of AtSOS1 (Salt Overly Sensitive 1), a plasma membrane Na+/H+-antiporter in Arabidopsis thaliana, leads to a salt-sensitive phenotype accompanied by the death of root cells under salt stress. Intracellular events and changes in gene expression were compared during a non-lethal salt stress between the wild type and a representative SOS1 mutant, atsos1-1, by confocal microscopy using ion-specific fluorophores and by quantitative RT-PCR. In addition to the higher accumulation of sodium ions, atsos1-1 showed inhibition of endocytosis, abnormalities in vacuolar shape and function, and changes in intracellular pH compared to the wild type in root tip cells under stress. Quantitative RT-PCR revealed a dramatically faster and higher induction of root-specific Ca2+ transporters, including several CAXs and CNGCs, and the drastic down-regulation of genes involved in pH-homeostasis and membrane potential maintenance. Differential regulation of genes for functions in intracellular protein trafficking in atsos1-1 was also observed. The results suggested roles of the SOS1 protein, in addition to its function as a Na+/H+ antiporter, whose disruption affected membrane traffic and vacuolar functions possibly by controlling pH homeostasis in root cells