RNA editing of nuclear transcripts in Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>RNA editing is a transcript-based layer of gene regulation. To date, no systemic study on RNA editing of plant nuclear genes has been reported. Here, a transcriptome-wide search for editing sites in nuclear transcripts of Arabidopsis (<it>Arabidopsis thaliana</it>) was performed.</p> <p>Results</p> <p>MPSS (massively parallel signature sequencing) and PARE (parallel analysis of RNA ends) data retrieved from public databases were utilized, focusing on one-base-conversion editing. Besides cytidine (C)-to-uridine (U) editing in mitochondrial transcripts, many nuclear transcripts were found to be diversely edited. Interestingly, a sizable portion of these nuclear genes are involved in chloroplast- or mitochondrion-related functions, and many editing events are tissue-specific. Some editing sites, such as adenosine (A)-to-U editing loci, were found to be surrounded by peculiar elements. The editing events of some nuclear transcripts are highly enriched surrounding the borders between coding sequences (CDSs) and 3′ untranslated regions (UTRs), suggesting site-specific editing. Furthermore, RNA editing is potentially implicated in new start or stop codon generation, and may affect alternative splicing of certain protein-coding transcripts. RNA editing in the precursor microRNAs (pre-miRNAs) of <it>ath-miR854</it> family, resulting in secondary structure transformation, implies its potential role in microRNA (miRNA) maturation.</p> <p>Conclusions</p> <p>To our knowledge, the results provide the first global view of RNA editing in plant nuclear transcripts.</p

Comparative RNA editing in autistic and neurotypical cerebella

Adenosine-to-inosine (A-to-I) RNA editing is a neurodevelopmentally regulated epigenetic modification shown to modulate complex behavior in animals. Little is known about human A-to-I editing, but it is thought to constitute one of many molecular mechanisms connecting environmental stimuli and behavioral outputs. Thus, comprehensive exploration of A-to-I RNA editing in human brains may shed light on gene–environment interactions underlying complex behavior in health and disease. Synaptic function is a main target of A-to-I editing, which can selectively recode key amino acids in synaptic genes, directly altering synaptic strength and duration in response to environmental signals. Here, we performed a high-resolution survey of synaptic A-to-I RNA editing in a human population, and examined how it varies in autism, a neurodevelopmental disorder in which synaptic abnormalities are a common finding. Using ultra-deep (>1000 × ) sequencing, we quantified the levels of A-to-I editing of 10 synaptic genes in postmortem cerebella from 14 neurotypical and 11 autistic individuals. A high dynamic range of editing levels was detected across individuals and editing sites, from 99.6% to below detection limits. In most sites, the extreme ends of the population editing distributions were individuals with autism. Editing was correlated with isoform usage, clusters of correlated sites were identified, and differential editing patterns examined. Finally, a dysfunctional form of the editing enzyme adenosine deaminase acting on RNA B1 was found more commonly in postmortem cerebella from individuals with autism. These results provide a population-level, high-resolution view of A-to-I RNA editing in human cerebella and suggest that A-to-I editing of synaptic genes may be informative for assessing the epigenetic risk for autism.Nancy Lurie Marks Family FoundationF. Hoffmann-La Roche & Co. (Applied Science Sequencing Grant Program)Autism Speaks (Organization)Simons FoundationNational Institutes of Health (U.S.) (Grant 1R01MH085143-01

Telomeres in Evolution and Development from Biosemiotic Perspective

Telomeres identify natural chromosome ends being different from broken DNA through differences in their &#x22;molecular syntax&#x22; (M.Eigen) which determines the functions of reverse transcriptase and its integrated RNA template, telomerase. Although telomeres play a crucial role in the linear chromosome organization of eukaryotic cells, their molecular syntax descended from an ancient retroviral competence. This is an indicator for the early retroviral colonization of large double stranded DNA viruses, which are putative ancestors of the eukaryotic nucleus.&#xd;&#xa;This talk will demonstrate certain advantages of the biosemiotic approach towards our evolutionary understanding of telomeres: focus on the genetic/genomic structures as language-like text which follows combinatorial (syntactic), context-sensitive (pragmatic) and&#xd;&#xa;content-specific (semantic) semiotic rules. Genetic/genomic organization from the biosemiotic perspective is not seen any longer as an object of randomly derived alterations (mutations) but as functional innovation coherent with the broad variety of natural genome editing competences of viruses.&#xd;&#xa

Split and Migrate: Resource-Driven Placement and Discovery of Microservices at the Edge

Microservices architectures combine the use of fine-grained and independently-scalable services with lightweight communication protocols, such as REST calls over HTTP. Microservices bring flexibility to the development and deployment of application back-ends in the cloud. Applications such as collaborative editing tools require frequent interactions between the front-end running on users\u27 machines and a back-end formed of multiple microservices. User-perceived latencies depend on their connection to microservices, but also on the interaction patterns between these services and their databases. Placing services at the edge of the network, closer to the users, is necessary to reduce user-perceived latencies. It is however difficult to decide on the placement of complete stateful microservices at one specific core or edge location without trading between a latency reduction for some users and a latency increase for the others. We present how to dynamically deploy microservices on a combination of core and edge resources to systematically reduce user-perceived latencies. Our approach enables the split of stateful microservices, and the placement of the resulting splits on appropriate core and edge sites. Koala, a decentralized and resource-driven service discovery middleware, enables REST calls to reach and use the appropriate split, with only minimal changes to a legacy microservices application. Locality awareness using network coordinates further enables to automatically migrate services split and follow the location of the users. We confirm the effectiveness of our approach with a full prototype and an application to ShareLatex, a microservices-based collaborative editing application

Spontaneous Embedding of DNA Mismatches Within the RNA:DNA Hybrid of CRISPR-Cas9.

CRISPR-Cas9 is the forefront technology for editing the genome. In this system, the Cas9 protein is programmed with guide RNAs to process DNA sequences that match the guide RNA forming an RNA:DNA hybrid structure. However, the binding of DNA sequences that do not fully match the guide RNA can limit the applicability of CRISPR-Cas9 for genome editing, resulting in the so-called off-target effects. Here, molecular dynamics is used to probe the effect of DNA base pair mismatches within the RNA:DNA hybrid in CRISPR-Cas9. Molecular simulations revealed that the presence of mismatched pairs in the DNA at distal sites with respect to the Protospacer Adjacent Motif (PAM) recognition sequence induces an extended opening of the RNA:DNA hybrid, leading to novel interactions established by the unwound nucleic acids and the protein counterpart. On the contrary, mismatched pairs upstream of the RNA:DNA hybrid are rapidly incorporated within the heteroduplex, with minor effect on the protein-nucleic acid interactions. As a result, mismatched pairs at PAM distal ends interfere with the activation of the catalytic HNH domain, while mismatches fully embedded in the RNA:DNA do not affect the HNH dynamics and enable its activation to cleave the DNA. These findings provide a mechanistic understanding to the intriguing experimental evidence that PAM distal mismatches hamper a proper function of HNH, explaining also why mismatches within the heteroduplex are much more tolerated. This constitutes a step forward in understanding off-target effects in CRISPR-Cas9, which encourages novel structure-based engineering efforts aimed at preventing the onset of off-target effects

Application of the bacteriophage Mu-driven system for the integration/amplification of target genes in the chromosomes of engineered Gram-negative bacteria—mini review

The advantages of phage Mu transposition-based systems for the chromosomal editing of plasmid-less strains are reviewed. The cis and trans requirements for Mu phage-mediated transposition, which include the L/R ends of the Mu DNA, the transposition factors MuA and MuB, and the cis/trans functioning of the E element as an enhancer, are presented. Mini-Mu(LR)/(LER) units are Mu derivatives that lack most of the Mu genes but contain the L/R ends or a properly arranged E element in cis to the L/R ends. The dual-component system, which consists of an integrative plasmid with a mini-Mu and an easily eliminated helper plasmid encoding inducible transposition factors, is described in detail as a tool for the integration/amplification of recombinant DNAs. This chromosomal editing method is based on replicative transposition through the formation of a cointegrate that can be resolved in a recombination-dependent manner. (E-plus)- or (E-minus)-helpers that differ in the presence of the trans-acting E element are used to achieve the proper mini-Mu transposition intensity. The systems that have been developed for the construction of stably maintained mini-Mu multi-integrant strains of Escherichia coli and Methylophilus methylotrophus are described. A novel integration/amplification/fixation strategy is proposed for consecutive independent replicative transpositions of different mini-Mu(LER) units with “excisable” E elements in methylotrophic cells

Preparation of survey data

This guide focuses on the data preparation phase, which starts after data collection and ends before their analysis. This first assessment of the “raw” survey data is crucial since data preparation can affect the quality of the data in a positive or negative way. After an overview of the different types of errors, the guide discusses the remedies and issues related to these editing procedures

3D-моделювання інструментів, процесу зняття припуску та формоутворення при двосторонньому торцевому шліфуванні некруглих деталей орієнтованими кругами

Запропоновано трьохмірне геометричне моделювання інструментів, процесу зняття припуску та формоутворення при двосторонньому торцевому шліфуванні циліндричних деталей з некруглим профілем. Шліфування деталей виконується орієнтованими профільованими шліфувальними кругами, які правляться перед обробкою. Комбінована правка включає правку ділянки для зняття чорнового припуску та калібруючої ділянки. У розроблених способах обробки торців циліндричних деталей з некруглим профілем досліджено вплив орієнтації деталей в барабані на їх точність.A three-dimensional geometric modeling of process tools, stock removal and shaping at the bilateral face grinding of cylindrical parts with a non-circular profile. Grinding parts performed oriented profiled grinding wheels, who ruled before processing. Combination editing includes editing area to remove rough allowance and the sizing section. The developed methods of processing the ends of cylindrical parts with a non-circular profile, investigated the influence of the orientation of parts in the drum on their accuracy

Semi-automatic Endogenous Enrichment of Collaboratively Constructed Lexical Resources: Piggybacking onto Wiktionary

International audienceThe lack of large-scale, freely available and durable lexical resources, and the consequences for NLP, is widely acknowledged but the attempts to cope with usual bottlenecks preventing their development often result in dead-ends. This article introduces a language-independent, semi-automatic and endogenous method for enriching lexical resources, based on collaborative editing and random walks through existing lexical relationships, and shows how this approach enables us to overcome recurrent impediments. It compares the impact of using different data sources and similarity measures on the task of improving synonymy networks. Finally, it defines an architecture for applying the presented method to Wiktionary and explains how it has been implemented