RNA-directed DNA methylation (RdDM) is an epigenetic process in plants that involves both short and long noncoding RNAs. The generation of these RNAs and the induction of RdDM rely on complex transcriptional machineries comprising two plant-specific, RNA polymerase II (Pol II)–related RNA polymerases known as Pol IV and Pol V, as well as a host of auxiliary factors that include both novel and refashioned proteins. We present current views on the mechanism of RdDM with a focus on evolutionary innovations that occurred during the transition from a Pol II transcriptional pathway, which produces mRNA precursors and numerous noncoding RNAs, to the Pol IV and Pol V pathways, which are specialized for RdDM and gene silencing. We describe recently recognized deviations from the canonical RdDM pathway, discuss unresolved issues, and speculate on the biological significance of RdDM for flowering plants, which have a highly developed Pol V pathway.

RNA-Directed DNA Methylation: The Evolution of a Complex Epigenetic Pathway in Flowering Plants.

A major part of the eukaryotic genome is transcribed into non-coding RNAs (ncRNAs) having no protein coding potential. ncRNAs which are longer than 200 nucleotides are categorized as long non coding RNAs (lncRNAs). Most lncRNAs are induced as a consequence of various environmental and developmental cues. Among plants, the functions of lncRNAs are best studied in Arabidopsis thaliana. In this review, we highlight the important functional roles of various lncRNAs during different stages of Arabidopsis life cycle and their response to environmental changes. These lncRNAs primarily govern processes such as flowering, seed germination, stress response, light- and auxin-regulated development, and RNA-dependent DNA methylation (RdDM). Major challenge is to differentiate between functional and cryptic transcripts. Genome editing, large scale RNAi and computational approaches may help to identify and characterize novel functional lncRNAs in Arabidopsis.

Functions of long non-coding RNA in Arabidopsis thaliana.

Reproductive tissues are a rich source of small RNAs, including several classes of short interfering (si)RNAs that are restricted to this stage of development. In addition to Pol IV-dependent 24-nt siRNAs that trigger canonical RNA-directed DNA methylation (RdDM), abundant reproductive-specific siRNAs are produced from companion cells adjacent to the developing germ line or zygote and may move intercellularly before inducing methylation. In some cases, these siRNAs are produced via non-canonical biosynthesis mechanisms or from sequences with little similarity to transposons. While the precise role of these siRNAs and the methylation they trigger is unclear, they have been implicated in specifying a single megaspore mother cell, silencing transposons in the male germ line, mediating parental dosage conflict to ensure proper endosperm development, hypermethylation of mature embryos, and trans-chromosomal methylation in hybrids. In this review, we summarize the current knowledge of reproductive siRNAs, including their biosynthesis, transport, and function.

https://academic.oup.com/plcell/article-pdf/35/6/1787/50481687/koad010.pdf

Small RNA-mediated DNA methylation during plant reproduction.

During plant embryogenesis, regardless of whether it begins with a fertilized egg cell (zygotic embryogenesis) or an induced somatic cell (somatic embryogenesis), significant epigenetic reprogramming occurs with the purpose of parental or vegetative transcript silencing and establishment of a next-generation epigenetic patterning. To ensure genome stability of a developing embryo, large-scale transposon silencing occurs by an RNA-directed DNA methylation (RdDM) pathway, which introduces methylation patterns de novo and as such potentially serves as a global mechanism of transcription control during developmental transitions. RdDM is controlled by a two-armed mechanism based around the activity of two RNA polymerases. While PolIV produces siRNAs accompanied by protein complexes comprising the methylation machinery, PolV produces lncRNA which guides the methylation machinery toward specific genomic locations. Recently, RdDM has been proposed as a dominant methylation mechanism during gamete formation and early embryo development in Arabidopsis thaliana, overshadowing all other methylation mechanisms. Here, we bring an overview of current knowledge about different roles of DNA methylation with emphasis on RdDM during plant zygotic and somatic embryogenesis. Based on published chromatin immunoprecipitation data on PolV binding sites within the A. thaliana genome, we uncover groups of auxin metabolism, reproductive development and embryogenesis-related genes, and discuss possible roles of RdDM at the onset of early embryonic development via targeted methylation at sites involved in different embryogenesis-related developmental mechanisms.

/pdf/taking-the-wheel-de-novo-dna-methylation-as-a-driving-force-2r9olxrj0o.pdf

Taking the Wheel - de novo DNA Methylation as a Driving Force of Plant Embryonic Development.

Java (de)serialization is prone to causing security-critical vulnerabilities that attackers can invoke existing methods (gadgets) on the application's classpath to construct a gadget chain to perform malicious behaviors. Several techniques have been proposed to statically identify suspicious gadget chains and dynamically generate injection objects for fuzzing. However, due to their incomplete support for dynamic program features (e.g., Java runtime polymorphism) and ineffective injection object generation for fuzzing, the existing techniques are still far from satisfactory. In this paper, we first performed an empirical study to investigate the characteristics of Java deserialization vulnerabilities based on our manually collected 86 publicly known gadget chains. The empirical results show that 1) Java deserialization gadgets are usually exploited by abusing runtime polymorphism, which enables attackers to reuse serializable overridden methods; and 2) attackers usually invoke exploitable overridden methods (gadgets) via dynamic binding to generate injection objects for gadget chain construction. Based on our empirical findings, we propose a novel gadget chain mining approach, GCMiner, which captures both explicit and implicit method calls to identify more gadget chains, and adopts an overriding-guided object generation approach to generate valid injection objects for fuzzing. The evaluation results show that GCMiner significantly outperforms the state-of-the-art techniques, and discovers 56 unique gadget chains that cannot be identified by the baseline approaches. 

pdf/improving-java-deserialization-gadget-chain-mining-via-32lt051m1w.pdf

Improving Java Deserialization Gadget Chain Mining via Overriding-Guided Object Generation

In higher plants the female germline is formed from the megaspore mother cell (MMC), a single cell in the pre-meiotic ovule. Previously, it was reported that mutants in RNA dependent DNA methylation - RdDM - pathway might be involved in restricting female germline to a single nucellus cell. We show that the DRM methyltransferase double mutant drm1drm2 also presents also presents ectopic enlarged cells, consistent with supernumerary MMC-like cells. In wild-type ovules MMC differentiation required SPOROCYTELESS/NOZZLE (SPL/NZZ), as demonstrated by the spl/nzz mutant failing to develop an MMC. We address the poorly understood upstream regulation of SPL/NZZ in ovules, showing that the RdDM pathway is important to restrict SPL/NZZ expression. In ago9, rdr6 and drm1drm2 mutants, SPL/NZZ is ectopically expressed, suggesting that the mutiple MMC-like cells observed might be due to the ectopic expression of SPL/NZZ. We show that the ovule identity gene SEEDSTICK, directly regulates the AGO9 and RDR6 expression in the ovule and therefore indirectly SPL/NZZ expression. A model is presented describing the network required to restrict SPL/NZZ expression to specify a single MMC.

/pdf/the-rna-dependent-dna-methylation-pathway-is-required-to-4hq44f9221.pdf

The RNA-dependent DNA methylation pathway is required to restrict SPOROCYTELESS/NOZZLE expression to specify a single female germ cell precursor in Arabidopsis.

Fruits are an important source of vitamins, minerals and nutrients in the human diet. They also contain several compounds of nutraceutical importance that have significant antioxidant and anti-inflammatory roles, which can protect the consumer from diseases, such as cancer, and cardiovascular disease as well as having roles in reducing the build-up of LDL-cholesterol in blood plasma and generally reduce the risks of disease and age-related decline in health. Cherries contain high concentrations of bioactive compounds and minerals, including calcium, phosphorous, potassium and magnesium, and it is, therefore, unsurprising that cherry consumption has a positive impact on health. This review highlights the development of sweet cherry fruit, the health benefits of cherry consumption, and the options for increasing consumer acceptance and consumption.

/pdf/fruit-development-in-sweet-cherry-3vjrpj2v.pdf

Fruit Development in Sweet Cherry

Deserialization of untrusted data is an issue in many programming languages. In particular, deserialization of untrusted data in Java can lead to Remote Code Execution attacks. Conditions for this type of attack exist, but vulnerabilities are hard to detect. In this paper, we propose a novel sandboxing approach for protecting Java applications based on trusted execution path used for defining the deserialization behavior. We test our defensive mechanism on two main Java Framework JBoss and Jenkins and we show the effectiveness and efficiency of our system. We also discuss the limitations of our current system on newer attacks strategies.

Trusted Execution Path for Protecting Java Applications Against Deserialization of Untrusted Data

Abstract Main conclusion This manuscript identifies cherry orthologues of genes implicated in the development of pericarpic fruit and pinpoints potential options and restrictions in the use of these targets for commercial exploitation of parthenocarpic cherry fruit. Abstract Cherry fruit contain a large stone and seed, making processing of the fruit laborious and consumption by the consumer challenging, inconvenient to eat ‘on the move’ and potentially dangerous for children. Availability of fruit lacking the stone and seed would be potentially transformative for the cherry industry, since such fruit would be easier to process and would increase consumer demand because of the potential reduction in costs. This review will explore the background of seedless fruit, in the context of the ambition to produce the first seedless cherry, carry out an in-depth analysis of the current literature around parthenocarpy in fruit, and discuss the available technology and potential for producing seedless cherry fruit as an ‘ultimate snacking product’ for the twenty-first century. 

/pdf/options-for-the-generation-of-seedless-cherry-the-ultimate-rgomai5p.pdf

Options for the generation of seedless cherry, the ultimate snacking product

In the last decade, we have seen the proliferation of code-reuse attacks that rely on deserialization of untrusted data in the context of web applications. The impact of these attacks is really important since they can be used for exposing private information of the users. In this paper, we design a tool for automatic discovery of deserialization vulnerabilities for the Java language. Our purpose is to devise an automatic methodology that use a set of program analysis techniques and is able to output a deserialization attack chain. We test our techniques against common Java libraries used in web technology. The execution of our tool on such a dataset was able to validate the attack chains for the majority of already known vulnerabilities, and it was also able to discover multiple novel chains that represent new types of attack vectors. 

JChainz: Automatic Detection of Deserialization Vulnerabilities for the Java Language

Handle everyday research tasks with reliable, citation-backed results

Your personal Research Agent to handle research tasks with citation-backed results

Popular Tasks used by Researchers

How can I help with your research?

Meet SciSpace

Get more enhanced response by uploading the PDFs you want me to reference.

No relevant PDFs in your library

SciSpace is the AI research assistant for academics. Run systematic literature reviews on 280M+ papers, and write papers with cited sources. Trusted by 1M+ students, PhDs & researchers.

SciSpace | AI for Research

Analyze PDFs

Code & Manuscripts

Funding & Grants

Literature & Patents

Medical & Clinical Data

Systematic Review

Visualize & Present

Web & Data

Build a Google Scholar-like website for your research.

Build a website

Create charts and images for your research

Create a Chart

Write a paper for submission to a journal

Draft a manuscript

Patent Search

Design eye-catching scientific posters in minutes.

Scientific Poster Generation

Systematic Literature Review

One task is running at the moment. Your messages will be shown right after.

Drag and drop or click here to browse

Loved by <highlight>1 million+</highlight> researchers

Extract a list of specific topics and their sources from unstructured text

Topics

Compare and analyze relevant papers that matches with your search

Papers

Get insights from PDFs and bookmarked papers from your library

My library

Recent searches

Try searching for:

Catch AI-generated content in scholarly and non-scholarly content

{ai} Detector

Ai Writer

Get PDF Summaries, highlighted text explanations 

Chat with PDF

Effortlessly create in-text citations and bibliographies in APA and 2,500 other formats

Citation generator

Get explanations, summaries, and answers on academic papers

Ease up your research workflow with {scispace}'s cohort of exciting AI tools

Elevate your academic writing skills and convey your ideas the way you want

Paraphraser

Explore our range of reading and writing tools

Your file is being prepared and should be ready in a few minutes. If it's a large file, it might take a bit longer. You can close this window, and we'll email you the file when it's done.

You have reached a maximum limit of <strong>{limit}</strong> columns in the table. Remove at least <strong>1</strong> column to add or create another one.

Edoardo Vignati

Author Tools

Chat about Author