392 research outputs found

    Comparative mitogenomic analyses of three scallops (Bivalvia: Pectinidae) reveal high level variation of genomic organization and a diversity of transfer RNA gene sets

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    <p>Abstract</p> <p>Background</p> <p>It can be seen from the available mollusk mitogenomes that the family Pectinidae exhibits the most variation in genome organization. In this study, comparative mitogenomic analyses were performed for three scallops from the subfamily Chlamydinae (Pectinidae), with the goal of characterizing the degree of variability of mitogenome organization and other characteristics among species from the same subfamily and exploring their possible evolution route.</p> <p>Findings</p> <p>The complete or nearly complete mtDNA sequences of scallop <it>Mimachlamys nobilis </it>(17 935 bp), <it>Mizuhopecten yessoensis </it>(20 964 bp) and <it>Chlamys farreri </it>(17 035 bp) were determined using long PCR amplification and primer walking sequencing strategy. Highly variable size difference of the three genomes resulted primarily from length and number variations of non-coding regions, and the major difference in gene content of the three scallop species are due to varying tRNA gene sets. Only 21, 16, and 17 tRNA genes were detected in the mitogenomes of <it>M. nobilis</it>, <it>M. yessoensis </it>and <it>C. farreri</it>, respectively. Remarkably, no <it>trnS </it>gene could be identified in any of the three scallops. A newly-detected <it>trnA</it>-like sequence within the mitogenome of <it>M. yessoensis </it>seems to exemplify the functional loss of a tRNA gene, and the duplication of <it>trnD </it>in <it>M. yessoensis </it>raises a fundamental question of whether the retention of the tRNA gene copy of 2-tRNAs is easier than that of 4-tRNAs. Analysis of putative evolutionary pathways of gene rearrangement indicates that transposition of neighboring gene blocks may play an important role in the evolution of mitogenomes in scallops. Parsimonious analysis of the genomic variations implies that the mitogenomes of <it>M. yessoensis </it>and <it>C. farreri </it>are likely to derive independently from a common ancestor that was closely related to <it>M. nobilis</it>.</p> <p>Conclusion</p> <p>Comparative mitogenomic analyses among three species from the subfamily Chlamydinae show that the three genomes exhibit a high level of genomic variation and a diversity of tRNA gene sets, characterized by extensive translocation of genes. These features provide useful clues and information for evolutionary analysis of scallop mitogenomes.</p

    Upregulated MicroRNA-29a by Hepatitis B Virus X Protein Enhances Hepatoma Cell Migration by Targeting PTEN in Cell Culture Model

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    Hepatitis B virus X protein (HBx) plays important roles in the development of hepatocellular carcinoma (HCC). MicroRNAs (miRNAs) contribute to cancer development by acting as oncogenes or tumor suppressors. Previously, we reported that HBx was able to promote the migration of hepatoma HepG2 cells. However, the regulation of miRNAs in the development of HBV-related HCC is poorly understood. In the present study, we reported that miR-29a was a novel regulator of migration of hepatoma cells mediated by HBx. Our data showed that the expression of miR-29a was dramatically increased in p21-HBx transgenic mice, HBx-transfected hepatoma HepG2-X (or H7402-X) cells and HepG2.2.15 cells that constitutively replicate HBV. However, our data showed that miR-29a was upregulated in 4 of the 11 clinical HCC samples. We found that the overexpression of miR-29a promoted the migration of HepG2 cells, while a specific miR-29a inhibitor could partially abolish the enhanced migration of HepG2-X cells. Moreover, we identified PTEN was one of the target genes of miR-29a in HepG2 cells. The deletion of the miR-29a-binding site was able to abolish the role of miR-29a in suppression of luciferase activity of the PTEN 3′UTR reporter. Meanwhile, the overexpression of PTEN was able to reverse the promoted migration of HepG2 cells mediated by miR-29a. Moreover, our data showed that the modulation of Akt phosphorylation, a downstream factor of PTEN, was involved in the cell migration enhanced by miR-29a, suggesting that miR-29a is responsible for the cell migration through its target gene PTEN. Thus, we conclude that miR-29a is involved in the regulation of migration of hepatoma cells mediated by HBx through PTEN in cell culture model

    Comparing the Usefulness of Distance, Monophyly and Character-Based DNA Barcoding Methods in Species Identification: A Case Study of Neogastropoda

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    DNA barcoding has recently been proposed as a promising tool for the rapid species identification in a wide range of animal taxa. Two broad methods (distance and monophyly-based methods) have been used. One method is based on degree of DNA sequence variation within and between species while another method requires the recovery of species as discrete clades (monophyly) on a phylogenetic tree. Nevertheless, some issues complicate the use of both methods. A recently applied new technique, the character-based DNA barcode method, however, characterizes species through a unique combination of diagnostic characters.Here we analyzed 108 COI and 102 16S rDNA sequences of 40 species of Neogastropoda from a wide phylogenetic range to assess the performance of distance, monophyly and character-based methods of DNA barcoding. The distance-based method for both COI and 16S rDNA genes performed poorly in terms of species identification. Obvious overlap between intraspecific and interspecific divergences for both genes was found. The “10× rule” threshold resulted in lumping about half of distinct species for both genes. The neighbour-joining phylogenetic tree of COI could distinguish all species studied. However, the 16S rDNA tree could not distinguish some closely related species. In contrast, the character-based barcode method for both genes successfully identified 100% of the neogastropod species included, and performed well in discriminating neogastropod genera.This present study demonstrates the effectiveness of the character-based barcoding method for species identification in different taxonomic levels, especially for discriminating the closely related species. While distance and monophyly-based methods commonly use COI as the ideal gene for barcoding, the character-based approach can perform well for species identification using relatively conserved gene markers (e.g., 16S rDNA in this study). Nevertheless, distance and monophyly-based methods, especially the monophyly-based method, can still be used to flag species

    Identification of dissociation factors in pancreatic Cancer using a mass spectrometry-based proteomic approach

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    Backgroud Pancreatic cancer is a highly malignant tumor of the digestive system. This secretome of pancreatic cancer is key to its progression and metastasis. But different methods of protein extraction affect the final results. In other words, the real secretion of proteins in cancer cells has been changed. Based on mass spectrometry, we analyze the secretome from the serum-containing and serum-free medium, using different protein pretreatment methods. This study aims to identify dissociation factors in pancreatic cancer. Methods In this study, pancreatic cancer cells were cultured in serum-containing or serum-free medium, and the corresponding supernatants were extracted as samples. Subsequently, the above samples were separated by size exclusion chromatography (SEC), and peptide segments were identified by LC-MS/MS. The final results were identified via the hamster secreted protein database and a public database. Results Although the number of identified proteins in the serum-free medium group was high, the real secretion of proteins in pancreatic cancer cells was changed. There were six significant secreted proteins in the serum-containing medium group. Survival analysis via the TCGA database suggested that patients with higher expression levels of YWHAG showed a worse overall survival rate than those with lower YWHAG expression. Conclusions Our study demonstrated the results in the serum-containing medium group were more similar to the real secretome of pancreatic cancer cells. YWHAG could be used as a prognostic indicator for pancreatic cancer

    Interpreting Distributional Reinforcement Learning: A Regularization Perspective

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    Distributional reinforcement learning~(RL) is a class of state-of-the-art algorithms that estimate the whole distribution of the total return rather than only its expectation. Despite the remarkable performance of distributional RL, a theoretical understanding of its advantages over expectation-based RL remains elusive. In this paper, we attribute the superiority of distributional RL to its regularization effect in terms of the value distribution information regardless of its expectation. Firstly, by leverage of a variant of the gross error model in robust statistics, we decompose the value distribution into its expectation and the remaining distribution part. As such, the extra benefit of distributional RL compared with expectation-based RL is mainly interpreted as the impact of a \textit{risk-sensitive entropy regularization} within the Neural Fitted Z-Iteration framework. Meanwhile, we establish a bridge between the risk-sensitive entropy regularization of distributional RL and the vanilla entropy in maximum entropy RL, focusing specifically on actor-critic algorithms. It reveals that distributional RL induces a corrected reward function and thus promotes a risk-sensitive exploration against the intrinsic uncertainty of the environment. Finally, extensive experiments corroborate the role of the regularization effect of distributional RL and uncover mutual impacts of different entropy regularization. Our research paves a way towards better interpreting the efficacy of distributional RL algorithms, especially through the lens of regularization

    Linearized Relative Positional Encoding

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    Relative positional encoding is widely used in vanilla and linear transformers to represent positional information. However, existing encoding methods of a vanilla transformer are not always directly applicable to a linear transformer, because the latter requires a decomposition of the query and key representations into separate kernel functions. Nevertheless, principles for designing encoding methods suitable for linear transformers remain understudied. In this work, we put together a variety of existing linear relative positional encoding approaches under a canonical form and further propose a family of linear relative positional encoding algorithms via unitary transformation. Our formulation leads to a principled framework that can be used to develop new relative positional encoding methods that preserve linear space-time complexity. Equipped with different models, the proposed linearized relative positional encoding (LRPE) family derives effective encoding for various applications. Experiments show that compared with existing methods, LRPE achieves state-of-the-art performance in language modeling, text classification, and image classification. Meanwhile, it emphasizes a general paradigm for designing broadly more relative positional encoding methods that are applicable to linear transformers. The code is available at https://github.com/OpenNLPLab/Lrpe.Comment: Reviewed by TMLR, decision pending. Yiran Zhong is the corresponding author. Code is available at https://github.com/OpenNLPLab/Lrp
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