1K Papers found (0.012 seconds)

Wang K et al. (2018) PeerJ "piRNN: deep learning algorithm for piRNA prediction."

[

PeerJ,

2018]

Piwi-interacting RNAs (piRNAs) are the largest class of small non-coding RNAs discovered in germ cells. Identifying piRNAs from small RNA data is a challenging task due to the lack of conserved sequences and structural features of piRNAs. Many programs have been developed to identify piRNA from small RNA data. However, these programs have limitations. They either rely on extracting complicated features, or only demonstrate strong performance on transposon related piRNAs. Here we proposed a new program called piRNN for piRNA identification. For our software, we applied a convolutional neural network classifier that was trained on the datasets from four different species (Caenorhabditis elegans, Drosophila melanogaster, rat and human). A matrix of k-mer frequency values was used to represent each sequence. piRNN has great usability and shows better performance in comparison with other programs. It is freely available at https://github.com/bioinfolabmu/piRNN.

Wang K et al. (2023) Mol Neurobiol "Hyperoside Prevents Aβ42-Induced Neurotoxicity in PC12 Cells and Caenorhabditis elegans."

Huang Q, Guo Q, Wang K, Li X, Wang J, Zhang X, Wang H, Liu S, Zhang M, Xie J

[

Mol Neurobiol,

2023]

Traditional Chinese medicines such as hyperoside-rich Acanthopanax senticosus and Crataegus pinnatifida have been confirmed to exhibit anti-oxidative stress properties. Hyperoside, the main ingredient of numerous antioxidant herbs, may have the ability to postpone the onset of neurodegenerative diseases. This study investigates the possible therapeutic mechanism of hyperoside as a natural antioxidant against Alzheimer's disease (AD) in Caenorhabditis elegans and PC12 cells. Specifically, hyperoside reduced reactive oxygen species (ROS) level and Aβ42-induced neurotoxicity in C. elegans worms. Meanwhile, hyperoside reduced ROS production and increased mitochondrial membrane potentialin Aβ42-induced PC12 cells, which possibly due to the increase of antioxidant enzymes activity and the diminution of malondialdehyde levels. Hoechst 33,342 staining and flow cytometry analysis results suggested that hyperoside reverses cell apoptosis. Network pharmacology predicts potentially relevant hyperoside targets and pathways in AD therapy. As anticipated, hyperoside reversed Aβ42-stimulated downregulation of the PI3K/Akt/Nrf2/HO-1. The PI3K inhibitor LY294002 partially abolished the protective capability of hyperoside. The results of molecular docking further indicated that the PI3K/Akt pathways may be involved in the protection of Aβ42-induced PC12 cells by hyperoside treatment. The study provides theoretical information for research and development of hyperoside as an antioxidant dietary supplement.

Wang K et al. (2023) Nat Biotechnol "PhyloVelo enhances transcriptomic velocity field mapping using monotonically expressed genes."

Zi Z, Zhai X, Wang X, Hu Z, Zhai W, Curtis C, Zhou D, Lu Z, He X, Wang K, Hou L

[

Nat Biotechnol,

2023]

Single-cell RNA sequencing (scRNA-seq) is a powerful approach for studying cellular differentiation, but accurately tracking cell fate transitions can be challenging, especially in disease conditions. Here we introduce PhyloVelo, a computational framework that estimates the velocity of transcriptomic dynamics by using monotonically expressed genes (MEGs) or genes with expression patterns that either increase or decrease, but do not cycle, through phylogenetic time. Through integration of scRNA-seq data with lineage information, PhyloVelo identifies MEGs and reconstructs a transcriptomic velocity field. We validate PhyloVelo using simulated data and Caenorhabditis elegans ground truth data, successfully recovering linear, bifurcated and convergent differentiations. Applying PhyloVelo to seven lineage-traced scRNA-seq datasets, generated using CRISPR-Cas9 editing, lentiviral barcoding or immune repertoire profiling, demonstrates its high accuracy and robustness in inferring complex lineage trajectories while outperforming RNA velocity. Additionally, we discovered that MEGs across tissues and organisms share similar functions in translation and ribosome biogenesis.

Wang K et al. (2018) Exp Gerontol "Enhanced ROS production leads to excessive fat accumulation through DAF-16 in Caenorhabditis elegans."

Huang J, Zhou H, Zhang C, Chen S, Lyu J, Qian X, Wang K, Wu J, Jin J, Jin L

[

Exp Gerontol,

2018]

Growing evidence shows that enhanced reactive oxygen species (ROS) production is an important contributor to obesity and its co-morbidities, but the functional link between ROS and obesity remains elusive. In this study we used the model animal Caenorhabditis elegans to explore the role of ROS in obesity. Initially, when ROS production was enhanced by treatment with low concentration of paraquat or juglone, both abnormal high fat accumulation and fatty acid composition were observed in wild type worms. We found that the abnormal fat accumulation was associated with increased expression of fat-5, which encodes an isoform of stearoyl-CoA synthetase, and which is regulated by daf-16 encoding the forkhead transcription factor and being activated by downregulation daf-2. When mutant daf-16 worms were used, the abnormal fat accumulation induced by ROS was suppressed. Collectively, we demonstrate that enhanced ROS production can lead to excessive fat accumulation and the change of fatty acid composition. This abnormal phenomenon at least in part depends on the daf-16 pathway by which fat-5 was regulated. The results point towards a role of ROS in obesity in the context of important conserved signaling pathway, thereby guide further studies and future therapeutic interventions.

Wang K et al. (2019) Int J Biol Macromol "Physicochemical characteristics and in vitro and in vivo antioxidant activity of a cell-bound exopolysaccharide produced by Lactobacillus fermentum S1."

Lu B, Wang K, Wu Y, Zhao J, Yao D, Zheng X, Niu M

[

Int J Biol Macromol,

2019]

A cell-bound exopolysaccharide (c-EPS) from Lactobacillus fermentum S1 was isolated and purified to near homogeneity by anion exchange and gel filtration chromatography. The c-EPS is a homogeneous heteropolysaccharide with an average molecular weight of 7.19x105Da and comprises mainly mannose, rhamnose, glucose, and galactose. Fourier transform infrared spectroscopy spectrum of the c-EPS exhibited typical characteristic absorption peaks of polysaccharides. Methylation and NMR analyses showed that the c-EPS had a backbone of -D-Galp-(13), -L-Rhap-(12), -D-Glcp-(13), -D-Galp-(13), -D-Glclp-(12), and -L-Rhap-(13,4) residues, terminated with -D-Manp-(1residue. The advanced structure study indicated the c-EPS not to have a triple-helical conformation, while the microstructural study revealed a hollow porous structure for c-EPS. Further, the thermal analysis showed that the degradation temperature for the c-EPS was 288.0C; its peak temperature was 89.4C with an enthalpy value of 273.1J/g. Moreover, the c-EPS exhibited potent DPPH, hydroxyl, and ABTS+ radicals scavenging activities, as well as FRAP in a dose-dependent manner, which could significantly enhance the T-AOC and SOD activity and reduce MDA level in Caenorhabditis elegans. Therefore, this c-EPS could be utilized as a promising natural antioxidant for application in functional foods.

Wang K et al. (2023) Int J Biol Macromol "Immunomodulatory activity and protective effect of a capsular polysaccharide in Caenorhabditis elegans, isolated from Lactobacillus fermentum GBJ."

Wang Y, Lu B, Sun J, Sun D, Pan Y, Zhao J, Gao Y, Zuo F, Wang K, Yao D, Tai M

[

Int J Biol Macromol,

2023]

A capsular polysaccharide, namely CPS-2, was isolated from Lactobacillus fermentum GBJ, purified using DEAE-52 anion exchange chromatography, and structurally characterized. We found that CPS-2 is homogenous, has an average molecular weight of 377 KDa, and is mainly composed of galactose and glucose at a molar ratio of 1.54:1.00. Its backbone comprises α-D-Galp-(1 → 3), α-D-Galp-(1 → 3,6), β-D-Glcp-(1 → 2), β-D-Galp-(1 → 6), and α-D-Galp-(1 → 4) residues with a side chain of β-D-Glcp-(1→). CPS-2 exerts an immunomodulatory effect by improving the proliferation and phagocytosis of macrophage RAW264.7 and promoting the secretion of NO and cytokines. The maximum secretion levels of IL-1β, IL-6, IL-10, and TNF-α were 1.96-, 0.11-, 0.22-, and 0.46-fold higher than those of the control, respectively. Furthermore, CPS-2 could significantly enhance the antioxidant system, extend lifespan, and improve stress tolerance of Caenorhabditis elegans at both exposure doses of 31.25 and 62.5 μg/mL. The average lifespan of nematodes reached a maximum in the 62.5 μg/mL-treated group after 10.39 days, 6.56 h, and 23.56 h in normal, oxidative stress, and heat shock environment, with extension percentages of 16.61 %, 43.23 %, and 15.77 %, respectively; therefore, CPS-2 displays an anti-aging effect. The significant bioactivity of CPS-2 promotes its application as a promising immunomodulatory and anti-aging ingredient in the food or pharmaceutical field.

Wang K et al. (2021) Anal Chim Acta "Design and synthesis of a novel "turn-on" long range measuring fluorescent probe for monitoring endogenous cysteine in living cells and Caenorhabditis elegans."

Wang W, Guo MY, Chen SY, Yang YS, Zhu HL, Xu C, Wang BZ, Wang K

[

Anal Chim Acta,

2021]

Cysteine (Cys) is an indispensable small organic molecule containing sulfhydryl groups, which has essential regulatory effects on the physiological process of human body. In this work, a red emission fluorescent probe TCFQ-Cys was designed and exploited based on 2-(3-cyano-4,5,5-trimethylfuran-2(5H)-ylidene) malononitrile-derivatives. The probe could effectively monitor Cys through the typical acrylate cleavage. The detecting system showed a red emission at 633nm and the fluorescence was stable within the pH range of 6-9. The detection could be completed in 30min. TCFQ-Cys presented high sensitivity with a detection limit of 0.133M and high selectivity towards Cys from other biological mercaptans. The most important feature was that the system had a wide linear range of 0-300M, which covered the physiological requirements of Cys detection. Subsequently, we conducted the biological imaging of Cys in MCF-7cells and Caenorhabditis elegans (C. elegans). Therefore, TCFQ-Cys had a practical application prospect for further investigating the physiological function of Cys.

(2015) Science "Erratum for the Report "Recruitment of RNA polymerase II by the pioneer transcription factor PHA-4" by H.-T. Hsu, H.-M. Chen, Z. Yang, J. Wang, N. K. Lee, A. Burger, K. Zaret, T. Liu, E. Levine, S. E. Mango."

[

Science,

2015]

Infarinato N (2019) J Cell Biol "Xiaochen Wang: Building up our understanding of breaking down."

Infarinato N

[

J Cell Biol,

2019]

Wang studies lysosomal degradation pathways using C. elegans as a model system.

Wang JT et al. (2014) Curr Biol "P granules."

Seydoux G, Wang JT

[

Curr Biol,

2014]

Wang and Seydoux discuss the functional importance of P granules - the germline-specific RNA granules of C. elegans.

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