HSP90ß Impedes STUB1-Induced Ubiquitination of YTHDF2 to Drive Sorafenib Resistance in Hepatocellular Carcinoma.

YTH domain family 2 (YTHDF2) is the first identified N6-methyladenosine (m6 A) reader that regulates the status of mRNA. It has been reported that overexpressed YTHDF2 promotes carcinogenesis; yet, its role in hepatocellular carcinoma (HCC) is elusive. Herein, it is demonstrated that YTHDF2 is upregulated and can predict poor outcomes in HCC. Decreased ubiquitination levels of YTHDF2 contribute to the upregulation of YTHDF2. Furthermore, heat shock protein 90 beta (HSP90ß) and STIP1 homology and U-box-containing protein 1 (STUB1) physically interact with YTHDF2 in the cytoplasm. Mechanically, the large and small middle domain of HSP90ß is required for its interaction with STUB1 and YTHDF2. HSP90ß inhibits the STUB1-induced degradation of YTHDF2 to elevate the expression of YTHDF2 and to further boost the proliferation and sorafenib resistance of HCC. Moreover, HSP90ß and YTHDF2 are upregulated, while STUB1 is downregulated in HCC tissues. The expression of HSP90ß is positively correlated with the YTHDF2 protein level, whereas the expression of STUB1 is negatively correlated with the protein levels of YTHDF2 and HSP90ß. These findings deepen the understanding of how YTHDF2 is regulated to drive HCC progression and provide potential targets for treating HCC.

An Efficient Synthesis of Naphtho[2,3-b]furan-4,9-diones via Visible-Light-Mediated [3+2] Cycloaddition Reaction.

Naphtho[2,3-b]furan-4,9-dione is an important privileged structural motif which is present in natural products, drugs, and drug candidates. Herein, visible-light-mediated [3+2] cycloaddition reaction for the synthesis of naphtho[2,3-b]furan-4,9-diones and dihydronaphtho[2,3-b]furan-4,9-diones has been developed. Under environmentally friendly conditions, a variety of title compounds were delivered in good yields. This new protocol shows excellent regioselectivity and remarkable functional group tolerance. This approach provides a powerful, green, efficient, and facile means to expand the structural diversity of naphtho[2,3-b]furan-4,9-diones and dihydronaph-tho[2,3-b]furan-4,9-diones as promising scaffolds for novel drug discovery.

Genome-wide identification of the valine-glutamine motif containing gene family and the role of VQ25-1 in pollen germination in Brassica oleracea.

BACKGROUND: The plant-specific valine-glutamine (VQ) motif containing proteins tightly regulate plant growth, development, and stress responses. However, the genome-wide identification and functional analysis of Brassica oleracea (B. oleracea) VQ genes have not been reported. OBJECTIVE: To identify the VQ gene family in B. oleracea and analyze the function of Bo25-1 in pollen germination. METHODS: The Hidden Markov Model (HMM) of VQ family was used to query the BoVQ genes in the B. oleracea genome. The BoVQ genes preferentially expressed in anthers were screened by qRT-PCR. Subcellular localization of VQ25-1 was observed in Nicotiana benthamiana (N. benthamiana) leaves. To analysis the role of BoVQ25-1 in pollen germination, the expression of BoVQ25-1 was suppressed using antisense-oligonucleotides (AS-ODN). RESULTS: A total of 64 BoVQ genes were identified in the B. oleracea genome. BoVQ25-1 was found to be preferentially expressed in the B. oleracea anthers. BoVQ25-1 was cloned from the anthers of the B. oleracea cultivar 'Fast Cycle'. BoVQ25-1 is localized to the nucleus. The pollen germination rate significantly decreased after AS-ODN treatment. CONCLUSION: Sixty-four BoVQ genes were identified in the B. oleracea genome, of which BoVQ25-1 plays an important role in pollen germination.

Genome assembly of wild loquat (Eriobotrya japonica) and resequencing provide new insights into the genomic evolution and fruit domestication in loquat.

Wild loquats (Eriobotrya japonica Lindl.) provide remarkable genetic resources for studying domestication and breeding improved varieties. Herein, we generate the first high-quality chromosome-level genome assembly of wild loquat, with 45 791 predicted protein-coding genes. Analysis of comparative genomics indicated that loquat shares a common ancestor with apple and pear, and a recent whole-genome duplication event occurred in loquat prior to its divergence. Genome resequencing showed that the loquat germplasms can be distinctly classified into wild and cultivated groups, and the commercial cultivars have experienced allelic admixture. Compared with cultivated loquats, the wild loquat genome showed very few selected genomic regions and had higher levels of genetic diversity. However, whole-genome scans of selective sweeps were mainly related to fruit quality, size, and flesh color during the domestication process. Large-scale transcriptome and metabolome analyses were further performed to identify differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in wild and cultivated loquats at various fruit development stages. Unlike those in wild loquat, the key DEGs and DAMs involved in carbohydrate metabolism, plant hormone signal transduction, flavonoid biosynthesis, and carotenoid biosynthesis were significantly regulated in cultivated loquats during fruit development. These high-quality reference genome, resequencing, and large-scale transcriptome/metabolome data provide valuable resources for elucidating fruit domestication and molecular breeding in loquat.

Genome-wide analysis of the WOX gene family and the role of EjWUSa in regulating flowering in loquat (Eriobotrya japonica).

The WUSCHEL (WUS)-related homeobox (WOX) gene family plays a crucial role in stem cell maintenance, apical meristem formation, embryonic development, and various other developmental processes. However, the identification and function of WOX genes have not been reported in perennial loquat. In this study, 18 EjWOX genes were identified in the loquat genome. Chromosomal localization analysis showed that 18 EjWOX genes were located on 12 of 17 chromosomes. Gene structure analysis showed that all EjWOX genes contain introns, of which 11 EjWOX genes contain untranslated regions. There are 8 pairs of segmental duplication genes and 0 pairs of tandem duplication genes in the loquat WOX family, suggesting that segmental duplications might be the main reason for the expansion of the loquat WOX family. A WOX transcription factor gene named EjWUSa was isolated from loquat. The EjWUSa protein was localized in the nucleus. Protein interactions between EjWUSa with EjWUSa and EjSTM were verified. Compared with wild-type Arabidopsis thaliana, the 35S::EjWUSa transgenic Arabidopsis showed early flowering. Our study provides an important basis for further research on the function of EjWOX genes and facilitates the molecular breeding of loquat early-flowering varieties.

Web Page Classification Algorithm Based on Deep Learning.

Transmit and process information to establish a learning mechanism and realize the processing of image data and sound data. However, the current research on Web page classification algorithm (WPCA) based on deep learning (DL) is not in-depth. Therefore, the main research of this article is the research of WPCA based on DL. This article first uses the keyword weight calculation method to reduce the impact of a small number of high-frequency words in the web page document on the weight calculation and reduces the value of the low-frequency word weights so that the WPCA is more accurate in the calculation process; second, the use of Chinese web pages: the classification method calculates the similarity between the text to be classified and all the class templates and then determines the category of all texts according to the similarity and certain classification rules; finally, in order to improve the learning rate of DL, consider using adaptive parameters. The optimization algorithm automatically adjusts the size of the learning rate, making the research of WPCA based on DL more efficient. After comparing the DL-based WPCA with the traditional algorithm, the data shows that in terms of time expenditure, the DL WPCA is 354 s, the traditional algorithm is 2436 s; in terms of memory overhead, the DL WPCA is 6.35 s, the traditional algorithm is 186.25 s. The experimental results show that WPCA based on DL are faster and more efficient than traditional algorithms and consume less system memory.

Intrinsic Decomposition Method Combining Deep Convolutional Neural Network and Probability Graph Model.

With the rapid development of computer vision and artificial intelligence, people are increasingly demanding image decomposition. Many of the current methods do not decompose images well. In order to find the decomposition method with high accuracy and accurate recognition rate, this study combines convolutional neural network and probability map model, and proposes a single-image intrinsic image decomposition method that is on both standard dataset images and natural images. Compared with the existing single-image automatic decomposition algorithm, the visual effect comparable to the user interaction decomposition algorithm is obtained, and the method of this study also obtains the lowest error rate in the quantitative comparison on the standard dataset image. The multi-image collaborative intrinsic image decomposition method proposed in this study obtains the decomposition result of consistent foreground reflectivity on multiple sets of image pairs. In this study, the eigenimage decomposition is applied to the illumination uniformity in the small change detection, and the promising reflectivity layer image obtained by the decomposition helps to improve the accuracy of the cooperative saliency detection. This study proposes an algorithm for the cooperation between CNN and probability graph model, and introduces how to combine the probability graph model with the traditional CNN to accomplish the pixel-level eigendecomposition task. This study also designs a single-image and multi-image intrinsic image decomposition results analysis experiments, then analyzes the probabilistic graphical model coordination intrinsic image decomposition results, and finally analyzes the convolutional neural network coordination intrinsic decomposition performance to draw the conclusion of this study. The effect on the Msrc-v2 dataset was increased by 0.8% over the probability plot model.

Distinct effects of mutations on biophysical properties of human prion protein monomers and oligomers.

Prion diseases are a group of fatal neurodegenerative illnesses, resulting from the conformational conversion of the cellular prion protein (PrPC) into a misfolded form (PrPSc). The formation of neurotoxic soluble prion protein oligomer (PrPO) is regarded as a key step in the development of prion diseases. About 10%-15% of human prion diseases are caused by mutations in the prion protein gene; however, the underlying molecular mechanisms remain unclear. In the present work, we compared the biophysical properties of wild-type (WT) human prion protein 91-231 (WT HuPrP91-231) and its disease-associated variants (P105L, D178N, V203I, and Q212P) using several biophysical techniques. In comparison with WT HuPrPC, the Q212P and D178N variants possessed greatly increased conversion propensities of PrPC into PrPO, while the V203I variant had dramatically decreased conversion propensity. The P105L variant displayed a similar conversion propensity to WT HuPrPC Guanidine hydrochloride-induced unfolding experiments ranked the thermodynamic stabilities of these proteins as Q212P < D178N < WT ≈ P105L < V203I. It was thus suggested that the conversion propensities of the prion proteins are closely associated with their thermodynamic stabilities. Furthermore, structural comparison illustrated that Q212P, D178N, and V203I variants underwent larger structural changes compared with WT HuPrPC, while the P105L variant adopted a similar structure to the WT HuPrPC The mutation-induced structural perturbations might change the thermodynamic stabilities of the HuPrPC variants, and correspondingly alter the conversion propensities for these prion proteins. Our results extend the mechanistic understanding of prion pathogenesis, and lay the basis for the prevention and treatment of prion diseases.

Unique Properties of the Rabbit Prion Protein Oligomer.

Prion diseases, also known as transmissible spongiform encephalopathies (TSEs), are a group of fatal neurodegenerative disorders infecting both humans and animals. Recent works have demonstrated that the soluble prion protein oligomer (PrPO), the intermediate of the conformational transformation from the host-derived cellular form (PrPC) to the disease-associated Scrapie form (PrPSc), exerts the major neurotoxicity in vitro and in vivo. Rabbits show strong resistance to TSEs, the underlying mechanism is unclear to date. It is expected that the relative TSEs-resistance of rabbits is closely associated with the unique properties of rabbit prion protein oligomer which remain to be addressed in detail. In the present work, we prepared rabbit prion protein oligomer (recRaPrPO) and human prion protein oligomer (recHuPrPO) under varied conditions, analyzed the effects of pH, NaCl concentration and incubation temperature on the oligomerization, and compared the properties of recRaPrPO and recHuPrPO. We found that several factors facilitated the formation of prion protein oligomers, including low pH, high NaCl concentration, high incubation temperature and low conformational stability of monomeric prion protein. RecRaPrPO was formed more slowly than recHuPrPO at physiological-like conditions (< 57°C, < 150 mM NaCl). Furthermore, recRaPrPO possessed higher susceptibility to proteinase K and lower cytotoxicity in vitro than recHuPrPO. These unique properties of recRaPrPO might substantially contribute to the TSEs-resistance of rabbits. Our work sheds light on the oligomerization of prion proteins and is of benefit to mechanistic understanding of TSEs-resistance of rabbits.

Distinct effects of Cu2+-binding on oligomerization of human and rabbit prion proteins.

The cellular prion protein (PrP(C)) is a kind of cell-surface Cu(2+)-binding glycoprotein. The oligomerization of PrP(C) is highly related to transmissible spongiform encephalopathies (TSEs). Cu(2+) plays a vital role in the oligomerization of PrP(C), and participates in the pathogenic process of TSE diseases. It is expected that Cu(2+)-binding has different effects on the oligomerization of TSE-sensitive human PrP(C) (HuPrP(C)) and TSE-resistant rabbit PrP(C) (RaPrP(C)). However, the details of the distinct effects remain unclear. In the present study, we measured the interactions of Cu(2+) with HuPrP(C) (91-230) and RaPrP(C) (91-228) by isothermal titration calorimetry, and compared the effects of Cu(2+)-binding on the oligomerization of both PrPs. The measured dissociation constants (Kd) of Cu(2+) were 11.1 ± 2.1 µM for HuPrP(C) and 21.1 ± 3.1 µM for RaPrP(C). Cu(2+)-binding promoted the oligomerization of HuPrP(C) more significantly than that of RaPrP(C). The far-ultraviolet circular dichroism spectroscopy experiments showed that Cu(2+)-binding induced more significant secondary structure change and increased more ß-sheet content for HuPrP(C) compared with RaPrP(C). Moreover, the urea-induced unfolding transition experiments indicated that Cu(2+)-binding decreased the conformational stability of HuPrP(C) more distinctly than that of RaPrP(C). These results suggest that RaPrP(C) possesses a low susceptibility to Cu(2+), potentially weakening the risk of Cu(2+)-induced TSE diseases. Our work sheds light on the Cu(2+)-promoted oligomerization of PrP(C), and may be helpful for further understanding the TSE-resistance of rabbits.