Identification of candidate genes involved in wax deposition in Poa pratensis by RNA-seq

A, Randomness test of cDNA fragments; B, Sequencing saturation analysis. T1 and T2 represent NEZm; T3 and T4 represent EBZ. (PDF 290 kb

Revisiting Scalarization in Multi-Task Learning: A Theoretical Perspective

Linear scalarization, i.e., combining all loss functions by a weighted sum, has been the default choice in the literature of multi-task learning (MTL) since its inception. In recent years, there is a surge of interest in developing Specialized Multi-Task Optimizers (SMTOs) that treat MTL as a multi-objective optimization problem. However, it remains open whether there is a fundamental advantage of SMTOs over scalarization. In fact, heated debates exist in the community comparing these two types of algorithms, mostly from an empirical perspective. To approach the above question, in this paper, we revisit scalarization from a theoretical perspective. We focus on linear MTL models and study whether scalarization is capable of fully exploring the Pareto front. Our findings reveal that, in contrast to recent works that claimed empirical advantages of scalarization, scalarization is inherently incapable of full exploration, especially for those Pareto optimal solutions that strike the balanced trade-offs between multiple tasks. More concretely, when the model is under-parametrized, we reveal a multi-surface structure of the feasible region and identify necessary and sufficient conditions for full exploration. This leads to the conclusion that scalarization is in general incapable of tracing out the Pareto front. Our theoretical results partially answer the open questions in Xin et al. (2021), and provide a more intuitive explanation on why scalarization fails beyond non-convexity. We additionally perform experiments on a real-world dataset using both scalarization and state-of-the-art SMTOs. The experimental results not only corroborate our theoretical findings, but also unveil the potential of SMTOs in finding balanced solutions, which cannot be achieved by scalarization.Comment: Accepted at NeurIPS 202

Species-Specific Expansion and Molecular Evolution of the 3-hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Plants

Kazakh dandelion (Taraxacum kok-saghyz, Tk) is a rubber-producing plant currently being investigated as a source of natural rubber for industrial applications. Like many other isoprenoids, rubber is a downstream product of the mevalonate pathway. The 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) enzyme catalyzes the conversion of 3-hydroxy-3-methylglutaryl-CoA to mevalonic acid, a key regulatory step in the MVA pathway. Such regulated steps provide targets for increases in isoprenoid and rubber contents via genetic engineering to increase enzyme activities. In this study, we identify a TkHMGR1 gene that is highly expressed in the roots of Kazakh dandelion, the main tissue where rubber is synthesized and stored. This finding paves the way for further molecular and genetic studies of the TkHMGR1 gene, and its role in rubber biosynthesis in Tk and other rubber-producing plants

Attitude control for the rigid spacecraft with the improved extended state observer

In this article, a three-axis attitude manoeuvre spacecraft consisting of a central rigid body and a rotating solar array is studied. The rotating solar array is considered a disturbance to the spacecraft. In the design of the controller, the coupled terms and the rotating solar array are considered a disturbance. The improved extended state observer is proposed by combing the sliding mode observer with the originally extended state observer to estimate the disturbance. The sliding mode control method is adopted to adjust the attitude of the spacecraft. Numerical simulations are presented to demonstrate the outstanding performance of the present observer

Systematic Identification and Validation of Suitable Reference Genes for the Normalization of Gene Expression in Prunella vulgaris under Different Organs and Spike Development Stages

The quantitative real-time PCR (qRT-PCR) is an efficient and sensitive method for determining gene expression levels, but the accuracy of the results substantially depends on the stability of the reference gene (RG). Therefore, choosing an appropriate reference gene is a critical step in normalizing qRT-PCR data. Prunella vulgaris L. is a traditional Chinese medicine herb widely used in China. Its main medicinal part is the fruiting spike which is termed Spica Prunellae. However, thus far, few studies have been conducted on the mechanism of Spica Prunellae development. Meanwhile, no reliable RGs have been reported in P. vulgaris. The expression levels of 14 candidate RGs were analyzed in this study in various organs and at different stages of Spica Prunellae development. Four statistical algorithms (Delta Ct, BestKeeper, NormFinder, and geNorm) were utilized to identify the RGs’ stability, and an integrated stability rating was generated via the RefFinder website online. The final ranking results revealed that eIF-2 was the most stable RG, whereas VAB2 was the least suitable as an RG. Furthermore, eIF-2 + Histon3.3 was identified as the best RG combination in different periods and the total samples. Finally, the expressions of the PvTAT and Pv4CL2 genes related to the regulation of rosmarinic acid synthesis in different organs were used to verify the stable and unstable RGs. The stable RGs in P. vulgaris were originally identified and verified in this work. This achievement provides strong support for obtaining a reliable qPCR analysis and lays the foundation for in-depth research on the developmental mechanism of Spica Prunellae

miR-429 suppresses tumor migration and invasion by targeting CRKL in hepatocellular carcinoma via inhibiting Raf/MEK/ERK pathway and epithelial-mesenchymal transition

Abstract Tumor metastasis is one of the main causes of hepatocellular carcinoma (HCC) high mortality. CRKL (v-crk sarcoma virus CT10 oncogene homologue (avian)-like) play important roles in tumor metastasis, however, the exact role and underlying mechanism of CRKL in HCC is still unknown. In our study, we demonstrated miR-429 negatively regulated CRKL expression via selectively binding to CRKL-3′-UTR at 3728–3735 bp site by post-transcriptionally mediating its functionality. Re-expression and silencing of miR-429 was remarkably effective in suppressing and promoting HepG2 cell migration and invasion in vitro. Knockdown or overexpression of CRKL exhibited similar effects as the overexpression or silencing of miR-429, whereas, CRKL overexpression (without the 3′-UTR) abrogated miR-429-induced inhibition on HepG2 migration and invasion. Moreover, miR-429-CRKL axis affected HepG2 migration and invasion potentials by regulating the adhesion ability, cytoskeleton F-actin expression and arrangement of HepG2. Furthermore, interference of Raf/MEK/ERK pathway and EMT contributed to miR-429-CRKL axis mediated metastasis inhibition. Nevertheless, miR-429 could not inhibit HepG2 proliferation through CRKL/c-Jun pathway. Taken together, our data demonstrated that miR-429 might function as an antimetastatic miRNA to regulate HCC metastasis by directly targeting CRKL via modulating Raf/MEK/ERK-EMT pathway. The newly identified miR-429-CRKL axis represents a novel potential therapeutic target for HCC treatment

Measuring circular phase-dichroism of chiral metasurface

The ability of chiral media to differentiate circularly polarized light is conventionally characterized by circular dichroism (CD) which is based on the difference in the absorption of the incident light for different polarizations. Thus, CD probes the bulk properties of chiral media. Here, we introduce a new approach termed as circular phase-dichroism that is based on the surface properties and is defined as the difference of the reflection phase for different circularly polarized incident lights in characterizing chiral media. As a demonstration, we measure the reflection phase from planar chiral sawtooth metasurface for circularly polarized light in the visible range using a simple Fabry Perot interference technique. The measured circular phase-dichroism is also crosschecked by conventional CD measurement of the transmitted light and by full-wave simulations. Our results demonstrate the potential applications of circular phase-dichroism in sensing and metasurface characterizations

Tetrahedral DNA Framework-Programmed Electrochemical Biosenors with Gold Nanoparticles for Ultrasensitive Cell-Free DNA Detection

Tumor-associated cell-free DNA (cfDNA) is a dynamic biomarker for genetic analysis, early diagnosis and clinical treatment of cancers. However, its detection has limitations because of its low abundance in blood or other complex bodily fluids. Herein, we developed an ultrasensitive cfDNA electrochemical biosensor (E-cfDNA sensor) based on tetrahedral DNA framework (TDF)-modified gold nanoparticles (Au NPs) with an interface for cfDNA detection. By accurately controlling the numbers of base pairs on each DNA framework, three types of TDFs were programmed: 26 base pairs of TDF; 17 base pairs of TDF; and 7 base pairs of TDF (TDF-26, TDF-16 and TDF-7, respectively). We also combined the TDF with hybridization chain reaction (HCR) to achieve signal amplification. Under optimal conditions, we detected the breast cancer susceptibility gene 1 (BRCA-1), a representative cfDNA closely related to breast cancer. An ultra-low detection limit of 1 aM with a linear range from 1 aM to 1 pM by TDF-26 was obtained, which was superior to the existing methods. Each type of TDF has excellent discrimination ability, which can distinguish single mismatch. More significantly, we also detected BRCA-1 in mimic serum samples, demonstrating that the E-cfDNA sensor has potential use in clinical research