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RNA secondary structure (RSS) can influence the regulation of transcription, RNA processing, and protein synthesis, among other processes. 3′ untranslated regions (3′ UTRs) of mRNA also hold the key for many aspects of gene regulation. However, there are often contradictory results regarding the roles of RSS in 3′ UTRs in gene expression in different organisms and/or contexts.

Here, we incidentally observe that the primary substrate of miR159a (pri-miR159a), when embedded in a 3′ UTR, could promote mRNA accumulation. The enhanced expression is attributed to the earlier polyadenylation of the transcript within the hybrid pri-miR159a-3′ UTR and, resultantly, a poorly structured 3′ UTR. RNA decay assays indicate that poorly structured 3′ UTRs could promote mRNA stability, whereas highly structured 3′ UTRs destabilize mRNA in vivo. Genome-wide DMS-MaPseq also reveals the prevailing inverse relationship between 3′ UTRs’ RSS and transcript accumulation in the transcriptomes ofArabidopsis, rice, and even human. Mechanistically, transcripts with highly structured 3′ UTRs are preferentially degraded by 3′–5′ exoribonuclease SOV and 5′–3′ exoribonuclease XRN4, leading to decreased expression inArabidopsis. Finally, we engineer different structured 3′ UTRs to an endogenousFTgene and alter theFT-regulated flowering time inArabidopsis.

We conclude that highly structured 3′ UTRs typically cause reduced accumulation of the harbored transcripts inArabidopsis. This pattern extends to rice and even mammals. Furthermore, our study provides a new strategy of engineering the 3′ UTRs’ RSS to modify plant traits in agricultural production and mRNA stability in biotechnology.

 

Abstract Eliciting informative user opinions from online reviews is a key success factor for innovative product design and development. The unstructured, noisy, and verbose nature of user reviews, however, often complicate large-scale need finding in a format useful for designers without losing important information. Recent advances in abstractive text summarization has created the opportunity to systematically generate opinion summaries from online reviews to inform the early stages of product design and development. However, two knowledge gaps hinder the applicability of opinion summarization methods in practice. First, there is a lack of formal mechanisms to guide the generative process with respect to different categories of product attributes and user sentiments. Second, the annotated training datasets needed for supervised training of abstractive summarization models are often difficult and costly to create. This article addresses these gaps by (1) devising an efficient computational framework for abstractive opinion summarization guided by specific product attributes and sentiment polarities, and (2) automatically generating a synthetic training dataset that captures various degrees of granularity and polarity. A hierarchical multi-instance attribute-sentiment inference mode is developed for assembling a high-quality synthetic dataset, which is utilized to fine-tune a pretrained language model for abstractive summary generation. Numerical experiments conducted on a large dataset scraped from three major e-Commerce retail store for apparel and footwear products indicate the performance, feasibility, and potentials of the developed framework. Several directions are provided for future exploration in the area of automated opinion summarization for user-centered design. 

Extracting and analyzing informative user opinion from large-scale online reviews is a key success factor in product design processes. However, user reviews are naturally unstructured, noisy, and verbose. Recent advances in abstractive text summrization provide an unprecedented opportunity to systematically generate summaries of user opinions to facilitate need finding for designers. Yet, two main gaps in the state-of-the-art opinion summarization methods limit their applicability to the product design domain. First is the lack of capabilities to guide the generative process with respect to various product aspects and user sentiments (e.g., polarity, subjectivity), and the second gap is the lack of annotated training datasets for supervised learning. This paper tackles these gaps by (1) devising an efficient and scalable methodology for abstractive opinion summarization from online reviews guided by aspects terms and sentiment polarities, and (2) automatically generating a reusable synthetic training dataset that captures various degrees of granularity and polarity. The methodology contributes a multi-instance pooling model with aspect and sentiment information integrated (MAS), a synthetic data assembled using the results of the MAS model, and a fine-tuned pretrained sequence-to-sequence model “T5” for summary generation. Numerical experiments are conducted on a large dataset scraped from a major e-commerce retail store for sneakers to demonstrate the performance, feasibility, and potentials of the developed methodology. Several directions are provided for future exploration in the area of automated opinion summarization for user-centered product design.

 

Metal additive manufacturing (AM) provides a platform for microstructure optimization via process control, but establishing a quantitative processing-microstructure linkage necessitates an efficient scheme for microstructure representation and regeneration. Here, we present a deep learning framework to quantitatively analyze the microstructural variations of metals fabricated by AM under different processing conditions. The principal microstructural descriptors are extracted directly from the electron backscatter diffraction patterns, enabling a quantitative measure of the microstructure differences in a reduced representation domain. We also demonstrate the capability of predicting new microstructures within the representation domain using a regeneration neural network, from which we are able to explore the physical insights into the implicitly expressed microstructure descriptors by mapping the regenerated microstructures as a function of principal component values. We validate the effectiveness of the framework using samples fabricated by a solid-state AM technology, additive friction stir deposition, which typically results in equiaxed microstructures. 

Abstract Background The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. Results We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. Conclusions Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species. 

Reproduction, the hallmark of biological activity, requires making an accurate copy of the genetic material to allow the progeny to inherit parental traits. In all living cells, the process of DNA replication is carried out by a concerted action of multiple protein species forming a loose protein–nucleic acid complex, the replisome. Proofreading and error correction generally accompany replication but also occur independently, safeguarding genetic information through all phases of the cell cycle. Advances in biochemical characterization of intracellular processes, proteomics, and the advent of single‐molecule biophysics have brought about a treasure trove of information awaiting to be assembled into an accurate mechanistic model of the DNA replication process. This review describes recent efforts to model elements of DNA replication and repair processes using computer simulations, an approach that has gained immense popularity in many areas of molecular biophysics but has yet to become mainstream in the DNA metabolism community. It highlights the use of diverse computational methods to address specific problems of the fields and discusses unexplored possibilities that lie ahead for the computational approaches in these areas.