Abstract
With the goal of charting plant transcriptional regulatory maps (i.e. transcription factors (TFs), cis-elements and interactions between them), we have upgraded the TF-centred database ...PlantTFDB (http://planttfdb.cbi.pku.edu.cn/) to a plant regulatory data and analysis platform PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) over the past three years. In this version, we updated the annotations for the previously collected TFs and set up a new section, ‘extended TF repertoires’ (TFext), to allow users prompt access to the TF repertoires of newly sequenced species. In addition to our regular TF updates, we are dedicated to updating the data on cis-elements and functional interactions between TFs and cis-elements. We established genome-wide conservation landscapes for 63 representative plants and then developed an algorithm, FunTFBS, to screen for functional regulatory elements and interactions by coupling the base-varied binding affinities of TFs with the evolutionary footprints on their binding sites. Using the FunTFBS algorithm and the conservation landscapes, we further identified over 20 million functional TF binding sites (TFBSs) and two million functional interactions for 21 346 TFs, charting the functional regulatory maps of these 63 plants. These resources are publicly available at PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) and a cloud-based mirror (http://plantregmap.gao-lab.org/), providing the plant research community with valuable resources for decoding plant transcriptional regulatory systems.
With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database ...PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/). In the new version, we identified 320 370 TFs from 165 species, presenting a more comprehensive genomic TF repertoires of green plants. Besides updating the pre-existing abundant functional and evolutionary annotation for identified TFs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant TF binding motifs derived from experiments; (ii) multiple types of regulatory elements identified from high-throughput sequencing data; (iii) regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements. In addition, we upgraded previous TF prediction server, and set up four novel tools for regulation prediction and functional enrichment analyses. Finally, we set up a novel companion portal PlantRegMap (http://plantregmap.cbi.pku.edu.cn) for users to access the regulation resource and analysis tools conveniently.
Abstract
The management of bacterial infections is becoming a major clinical challenge due to the rapid evolution of antibiotic resistant bacteria. As an excellent candidate to overcome antibiotic ...resistance, antimicrobial peptides (AMPs) that are produced from the synthetic and natural sources demonstrate a broad-spectrum antimicrobial activity with the high specificity and low toxicity. These peptides possess distinctive structures and functions by employing sophisticated mechanisms of action. This comprehensive review provides a broad overview of AMPs from the origin, structural characteristics, mechanisms of action, biological activities to clinical applications. We finally discuss the strategies to optimize and develop AMP-based treatment as the potential antimicrobial and anticancer therapeutics.
Melatonin regulates broad aspects of plant responses to various biotic and abiotic stresses, but the upstream regulation of melatonin biosynthesis by these stresses remains largely unknown. Herein, ...we demonstrate that transcription factor heat‐shock factor A1a (HsfA1a) conferred cadmium (Cd) tolerance to tomato plants, in part through its positive role in inducing melatonin biosynthesis under Cd stress. Analysis of leaf phenotype, chlorophyll content, and photosynthetic efficiency revealed that silencing of the HsfA1a gene decreased Cd tolerance, whereas its overexpression enhanced plant tolerance to Cd. HsfA1a‐silenced plants exhibited reduced melatonin levels, and HsfA1a overexpression stimulated melatonin accumulation and the expression of the melatonin biosynthetic gene caffeic acid O‐methyltransferase 1 (COMT1) under Cd stress. Both an in vitro electrophoretic mobility shift assay and in vivo chromatin immunoprecipitation coupled with qPCR analysis revealed that HsfA1a binds to the COMT1 gene promoter. Meanwhile, Cd stress induced the expression of heat‐shock proteins (HSPs), which was compromised in HsfA1a‐silenced plants and more robustly induced in HsfA1a‐overexpressing plants under Cd stress. COMT1 silencing reduced HsfA1a‐induced Cd tolerance and melatonin accumulation in HsfA1a‐overexpressing plants. Additionally, the HsfA1a‐induced expression of HSPs was partially compromised in COMT1‐silenced wild‐type or HsfA1a‐overexpressing plants under Cd stress. These results demonstrate that HsfA1a confers Cd tolerance by activating transcription of the COMT1 gene and inducing accumulation of melatonin that partially upregulates expression of HSPs.
With advances in next-generation sequencing technologies, numerous novel transcripts in a large number of organisms have been identified. With the goal of fast, accurate assessment of the coding ...ability of RNA transcripts, we upgraded the coding potential calculator CPC1 to CPC2. CPC2 runs ∼1000 times faster than CPC1 and exhibits superior accuracy compared with CPC1, especially for long non-coding transcripts. Moreover, the model of CPC2 is species-neutral, making it feasible for ever-growing non-model organism transcriptomes. A mobile-friendly web server, as well as a downloadable standalone package, is freely available at http://cpc2.cbi.pku.edu.cn.
Robust, ultrathin, and environmental‐friendliness papers that synergize high‐efficiency electromagnetic interference (EMI) shielding, personal thermal management, and wearable heaters are essential ...for next‐generation smart wearable devices. Herein, MXene nanocomposite paper with a nacre‐like structure for EMI shielding and electrothermal/photothermal conversion is fabricated by vacuum filtration of Ti3C2Tx MXene and modified sawdust. The hydrogen bonding and highly oriented structure enhance the mechanical properties of the modified sawdust/MXene composite paper (SM paper). The SM paper with 50 wt% MXene content shows a strength of 23 MPa and a toughness of 13 MJ·M−3. The conductivity of the SM paper is 10 195 S·m−1, resulting in an EMI shielding effectiveness (SE) of 67.9 dB and a specific SE value (SSE/t) of 8486 dB·cm2·g−1. In addition, the SM paper exhibits excellent thermal management performance including high light/electro‐to‐thermal conversion, rapid Joule heating and photothermal response, and sufficient heating stability. Notably, the SM paper exhibits low infrared emissivity and distinguished infrared stealth performance, camouflaging a high‐temperature heater surface of 147–81 °C. The SM‐based e‐skin achieves visualization of Joule heating and realizes human motions monitoring. This work presents a new strategy for designing MXene‐based wearable devices with great EMI shielding, artificial intelligence, and thermal management applications.
A TDS/MXene (SM) paper is prepared by Ti3C2Tx and modified sawdust as the smart wearable device, showing a strength of 23 MPa and an EMI SE of 67.9 dB. The SM paper achieves a high Joule heating and photothermal temperature and exhibits notable infrared stealth performance, camouflaging a high‐temperature. The paper‐based e‐skin visualizes Joule heating temperature and monitors human motions.
Melatonin is a pleiotropic signal molecule that plays critical roles in regulating plant growth and development, as well as providing physiological protections against various environmental stresses. ...Nonetheless, the mechanisms for melatonin-mediated pollen thermotolerance remain largely unknown. In this study, we report that irrigation treatment with melatonin (20 µM) effectively ameliorated high temperature-induced inactivation of pollen and inhibition of pollen germination in tomato (
) plants. Melatonin alleviated reactive oxygen species production in tomato anthers under high temperature by the up-regulation of the transcription and activities of several antioxidant enzymes. Transmission electron micrograph results showed that high temperature-induced pollen abortion is associated with a premature degeneration of the tapetum cells and the formation of defective pollen grains with degenerated nuclei at the early uninuclear microspore stage, whilst melatonin protected degradation of organelles by enhancing the expression of heat shock protein genes to refold unfolded proteins and the expression of autophagy-related genes and formation of autophagosomes to degrade denatured proteins. These findings suggest a novel function of melatonin to protect pollen activity under high temperature and support the potential effects of melatonin on reproductive development of plants.
Melittin is a natural polypeptide present in bee venom, with significant anti-tumor activity. Melittin has been reported to induce cell death in lung carcinoma cell line A549 cells, suggesting an ...excellent potential for treating lung cancer. However, the core mechanism underlying melittin-induced cell death in A549 cells remains unclear. This work reports that melittin induces reactive oxygen species (ROS) burst, upregulates intracellular Fe
2+
levels, disrupts the glutathione-glutathione peroxidase 4 antioxidant system, and increases lipid peroxide accumulation, eventually inducing cell death, indicating that ferroptosis may be involved in the antitumor effects of melittin in A549 cells. Furthermore, A549 cells treated with the ferroptosis inhibitors ferrostatin-1 and deferoxamine demonstrated that these inhibitors could reverse the cell death induced by melittin, further confirming that melittin induces A549 cell death via ferroptosis. Furthermore, the results also illustrated that melittin activated the endoplasmic reticulum (ER) stress-CHOP (C/EBP homologous protein) apoptotic signal, closely associated with high-level intracellular ROS. The ER stress inhibitor, 4-Phenylbutyric acid, was used to confirm that ER stress-CHOP apoptotic signaling is another molecular mechanism of melittin-induced A549 cell death. Thus, our results demonstrate that ferroptosis and ER stress-CHOP signaling are key molecular mechanisms of melittin-induced cell death in lung cancer.
KEY POLICY HIGHLIGHTS
Melittin upregulates intracellular Fe
2+
levels, leading to the accumulation of lipid peroxides in A549 cells.
Melittin disrupts the glutathione-glutathione peroxidase 4 antioxidant system in A549 cells.
Melittin induces activation of endoplasmic reticulum stress-C/EBP homologous protein apoptosis signal.
Ferroptosis and ER stress are the core molecular mechanisms underlying melittin-induced cell death in A549 cells.
Celotno besedilo
Dostopno za:
BFBNIB, DOBA, GIS, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Janus MXene-decorated CNFs/luffa (JMCL) aerogel integrated the multifunction of fast water transport, good thermal management, fast vapor escape, and efficient photothermal conversion in a ...single-module. The hydrophobic lower part and hydrophilic upper part perform complementary functions, endowing the JMCL aerogel with high sunlight-to-heat-to-vapor conversion efficiency and self-floating performance. The JMCL aerogels delivered a water evaporation rate of 1.40 kg m-2h−1 and an efficiency of 91.20% under 1 sun illumination. In addition, the mechanical strength of JMCL aerogels is 437 times that of MXene/CNFs aerogels. The excellent salt resistance during 24h working and long-term solar vapor generation of up to 28 days were achieved.
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Interfacial solar steam generation (ISSG) is considered to be an attractive technique to address the water shortage. However, developing a sustainable thermal management, salt rejection, and excellent mechanical strength ISSG device for long-term stability desalination is still a challenge. Herein, a biomass ISSG device with superb mechanical properties was prepared by introducing a luffa sponge as the skeleton and constructing the MXene/cellulose nanofibers (CNFs) aerogels via freeze-drying. The Janus MXene-decorated CNFs/luffa (JMCL) aerogels integrated the multifunction of fast water transport, good thermal management, and efficient photothermal conversion in a single module, to achieve high-efficiency desalination. 3D Janus structure endowed the JMCL aerogel with opposite wettability, which is feasible to construct the localized photothermal generation and self-floating. The mechanical strength of JMCL aerogels is 437 times that of MXene/CNFs aerogels. The JMCL aerogels delivered a water evaporation rate of 1.40 kg m-2h−1 and an efficiency of 91.20% under 1 sun illumination. The excellent salt resistance during 24 h working and long-term solar vapor generation of up to 28 days were achieved. The multifunctional JMCL aerogels with 3D Janus structure offer new insights for developing good durability and eco-friendly biopolymer-based steam generators.
RNA molecules contain diverse modifications that display important functions in a variety of physiological and pathological processes. So far over 150 chemical modifications have been characterized ...to be present in various RNA species, such as in messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). Previous studies revealed that certain RNA modifications were correlated to specific human diseases, indicating RNA modifications could serve as the potential indicator of human diseases. However, systemic investigation of the alteration of RNA modifications in different RNA species of carcinoma tissues are still lacked. Herein, we carried out the comprehensive profiling and evaluation of the alteration of RNA modifications in thyroid carcinoma by liquid chromatography-tandem mass spectrometry (LC-ESI-MS/MS) analysis. The developed method allowed us to simultaneously detect 48 different types of RNA modifications. Using this method, we detected 10, 15, 14, and 25 modifications in mRNA, 18S rRNA, 28S rRNA and small RNA (< 200 nt), respectively. Compared to the normal tissues, we revealed a total of 14 RNA modification exhibited significant increase and 2 RNA modifications showed significant decrease in thyroid carcinoma tissues. Our study provided the first comprehensive profile as well as the alteration of modifications in different RNA species in thyroid carcinoma and matched tumor-adjacent normal tissues. The altered pattern RNA modifications may serve as the indicator of thyroid carcinoma. Moreover, this study may promote the in-depth understanding of the regulatory roles of RNA modifications in thyroid carcinoma.
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We carried out the comprehensive profiling and evaluation of the alteration of RNA modifications in thyroid carcinoma by LC-ESI-MS/MS analysis. The quantification results showed that a total of 14 RNA modification exhibited significant increase and 2 RNA modifications showed significant decrease in thyroid carcinoma tissues, which lays a foundation for diagnosis, monitoring disease evolution, and predicting response to treatment through specific RNA modification patterns.
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