PRIN: a predicted rice interactome network

<p>Abstract</p> <p>Background</p> <p>Protein-protein interactions play a fundamental role in elucidating the molecular mechanisms of biomolecular function, signal transductions and metabolic pathways of living organisms. Although high-throughput technologies such as yeast two-hybrid system and affinity purification followed by mass spectrometry are widely used in model organisms, the progress of protein-protein interactions detection in plants is rather slow. With this motivation, our work presents a computational approach to predict protein-protein interactions in <it>Oryza sativa</it>.</p> <p>Results</p> <p>To better understand the interactions of proteins in <it>Oryza sativa</it>, we have developed PRIN, a Predicted Rice Interactome Network. Protein-protein interaction data of PRIN are based on the interologs of six model organisms where large-scale protein-protein interaction experiments have been applied: yeast (<it>Saccharomyces cerevisiae</it>), worm (<it>Caenorhabditis elegans</it>), fruit fly (<it>Drosophila melanogaster</it>), human (<it>Homo sapiens</it>), <it>Escherichia coli </it>K12 and <it>Arabidopsis thaliana</it>. With certain quality controls, altogether we obtained 76,585 non-redundant rice protein interaction pairs among 5,049 rice proteins. Further analysis showed that the topology properties of predicted rice protein interaction network are more similar to yeast than to the other 5 organisms. This may not be surprising as the interologs based on yeast contribute nearly 74% of total interactions. In addition, GO annotation, subcellular localization information and gene expression data are also mapped to our network for validation. Finally, a user-friendly web interface was developed to offer convenient database search and network visualization.</p> <p>Conclusions</p> <p>PRIN is the first well annotated protein interaction database for the important model plant <it>Oryza sativa</it>. It has greatly extended the current available protein-protein interaction data of rice with a computational approach, which will certainly provide further insights into rice functional genomics and systems biology.</p> <p>PRIN is available online at <url>http://bis.zju.edu.cn/prin/</url>.</p

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

Democratizing Large Language Models via Personalized Parameter-Efficient Fine-tuning

Personalization in large language models (LLMs) is increasingly important, aiming to align LLM's interactions, content, and recommendations with individual user preferences. Recent advances in LLM personalization have spotlighted effective prompt design, by enriching user queries with non-parametric knowledge through behavior history retrieval and textual profiles. However, these approaches were limited due to a lack of model ownership, resulting in constrained customization and privacy issues. Moreover, they often failed to accurately capture user behavior patterns, especially in cases where user data were complex and dynamic. To address these shortcomings, we introduce One PEFT Per User (OPPU), which employs personalized parameter-efficient fine-tuning (PEFT) modules, to store user-specific behavior patterns and preferences. By plugging in users' personal PEFT parameters, they can own and use their LLMs personally. OPPU integrates parametric user knowledge in the personal PEFT parameters with the non-parametric knowledge acquired through retrieval and profile. This integration adapts individual LLMs to user behavior shifts. Experimental results demonstrate that OPPU significantly outperforms existing prompt-based methods across seven diverse tasks in the LaMP benchmark. Further in-depth studies reveal OPPU's enhanced capabilities in handling user behavior shifts, modeling users at different active levels, maintaining robustness across various user history formats, and displaying versatility with different PEFT methods

Ownership guided C to Rust translation

Dubbed a safer C, Rust is a modern programming language that combines memory safety and low-level control. This interesting combination has made Rust very popular among developers and there is a growing trend of migrating legacy codebases (very often in C) to Rust. In this paper, we present a C to Rust translation approach centred around static ownership analysis. We design a suite of analyses that infer ownership models of C pointers and automatically translate the pointers into safe Rust equivalents. The resulting tool, Crown, scales to real-world codebases (half a million lines of code in less than 10 seconds) and achieves a high conversion rate

Tracking microRNA Processing Signals by Degradome Sequencing Data Analysis

Degradome sequencing (degradome-seq) was widely used for cleavage site mapping on the microRNA (miRNA) targets. Here, the application value of degradome-seq data in tracking the miRNA processing intermediates was reported. By adopting the parameter “signal/noise” ratio, prominent degradome signals on the miRNA precursors were extracted. For the 15 species analyzed, the processing of many miRNA precursors were supported by the degradome-seq data. We found that the supporting ratio of the “high-confidence” miRNAs annotated in miRBase was much higher than that of the “low-confidence.” For a specific species, the percentage of the miRNAs with degradome-supported processing signals was elevated by the increment of degradome sampling diversity. More interestingly, the tissue- or cell line-specific processing patterns of the miRNA precursors partially contributed to the accumulation patterns of the mature miRNAs. In this study, we also provided examples to show the value of the degradome-seq data in miRNA annotation. Based on the distribution of the processing signals, a renewed model was proposed that the stems of the miRNA precursors were diced through a “single-stranded cropping” mode, and “loop-to-base” processing was much more prevalent than previously thought. Together, our results revealed the remarkable capacity of degradome-seq in tracking miRNA processing signals

Вирусная реклама как средство привлечения внимания к услугам организации

ВКР посвящена изучению вирусной рекламы как средства привлечения внимания к услугам организации. Автором был разработан комплекс необходимых рекламных продуктов и мероприятий для привлечения внимания к услугам магазина детских товаров нового сегмента целевой аудитории

Homozygous mutation in DNAAF4 causes primary ciliary dyskinesia in a Chinese family

Primary ciliary dyskinesia (PCD) is a rare autosomal recessive disorder that affects the structure and function of motile cilia, leading to classic clinical phenotypes, such as situs inversus, chronic sinusitis, bronchiectasis, repeated pneumonia and infertility. In this study, we diagnosed a female patient with PCD who was born in a consanguineous family through classic clinical manifestations, transmission electron microscopy and immunofluorescence staining. A novel DNAAF4 variant NM_130810: c.1118G&gt;A (p. G373E) was filtered through Whole-exome sequencing. Subsequently, we explored the effect of the mutation on DNAAF4 protein from three aspects: protein expression, stability and interaction with downstream DNAAF2 protein through a series of experiments, such as transfection of plasmids and Co-immunoprecipitation. Finally, we confirmed that the mutation of DNAAF4 lead to PCD by reducing the stability of DNAAF4 protein, but the expression and function of DNAAF4 protein were not affected

Large-Scale Identification of Mirtrons in Arabidopsis and Rice

A new catalog of microRNA (miRNA) species called mirtrons has been discovered in animals recently, which originate from spliced introns of the gene transcripts. However, only one putative mirtron, osa-MIR1429, has been identified in rice (Oryza sativa). We employed a high-throughput sequencing (HTS) data- and structure-based approach to do a genome-wide search for the mirtron candidate in both Arabidopsis (Arabidopsis thaliana) and rice. Five and eighteen candidates were discovered in the two plants respectively. To investigate their biological roles, the targets of these mirtrons were predicted and validated based on degradome sequencing data. The result indicates that the mirtrons could guide target cleavages to exert their regulatory roles post-transcriptionally, which needs further experimental validation

Radiated tumor cell-derived microparticles effectively kill stem-like tumor cells by increasing reactive oxygen species

Stem-like tumor cells (SLTCs) are thought to be the cellular entity responsible for clinical recurrence and subsequent metastasis. Inhibiting or killing SLTCs can effectively reduce recurrence and metastasis, yet little has been done to clear SLTCs because they are usually resistant to chemotherapy, radiotherapy, and even immunotherapy. In this study, we established SLTCs by low-serum culture and confirmed that the low-serum-cultured tumor cells were in a quiescent state and resistant to chemotherapy, showing features of SLTCs, consistent with the reported data. We demonstrated that SLTCs had high levels of reactive oxygen species (ROS). Based on the finding that radiated tumor cell-derived microparticles (RT-MPs) contained ROS, we used RT-MPs to kill SLTCs. We found that RT-MPs could further increase ROS levels and kill SLTCs in vivo and in vitro partially by ROS carried by the RT-MPs themselves, providing a new method for eliminating SLTCs