Co-extraction of high-quality RNA and DNA from rubber tree (Hevea brasiliensis)

High-quality nucleic acids are the basic requirement for performing genomic research. A reliable and efficient method was developed for co-extracting high-quality DNA and RNA from rubber tree (Hevea brasiliensis) in this study. Polyethylene glycol (PEG) and cetyltrimethylammonium bromide (CTAB) extraction buffer with high concentrations of polyvinylpyrrolidone (PVP) and β-mercaptoethanol was used in this study. The results show that 3.2% polyethylene glycol 8000 is the optimal concentration for successful separation of DNA and RNA. Spectrophotometric determination (A260/A280 and A260/A230 ratios), agarose electrophoresis analysis and reverse transcription (RT-PCR) of isolated nucleic acids indicate that high-quality DNA and RNA were extracted by this method. The general applicability of this method was also evaluated, and the results show that it was suitable for a variety of plants.Key words: Hevea brasiliensis, polyethylene glycol (PEG), nucleic acid, co-extraction, higher plants

Grey Relational Analysis on Yield-Related Traits of Wild Germplasm Resources of Hevea brasiliensis

【Objective】Natural rubber is an important industrial raw materials and strategic materials, and played a very important role in national economic development. As a resource constraint industry, it was mainly produced by Brazilian rubber tree (Hevea brasiliensis) and it has the highest yield and the best quality among the mankind known rubber-producing plants. Harvesting latex is the main economic purpose of Brazilian rubber tree, latex yield is a quantitative trait controlled by minorgene, with many influencing factors, and its phenotypic value is affected by heredity and environmental effect. To determine the relationship among the yield and agronomic traits of the wild germplasm resources of Hevea brasiliensis, this study provides a scientific basis for the evaluation and screening of rubber tree germplasm resources and the selection and breeding of new varieties.【Method】The yield, growth and other related agronomic traits of 13 wild germplasm resources of Hevea brasiliensis planted in the experimental field of Chinese Academy of Tropical Agricultural Sciences (CATAS) were studied and analyzed by grey relational analysis.【Result】The results showed that the association order of the eight main agronomic traits related to the dry rubber yield per plant were stem girth, dry rubber content, average number of laticifer cells, average number of laticifer columns, bark thickness, mean stem girth increment, lateral vein latex grade and gum value ratio, and the weights of each trait were 0.1380, 0.1338, 0.1322, 0.1264, 0.1205, 0.1182, 0.1178, 0.1143. In summary, stem girth, dry rubber content, quantity of laticifers bark thickness and other traits are closely related to and have a great impact on dry rubber yield per plant.【Conclusion】Among the main agronomic traits, the stem girth, dry rubber content and quantity of laticifer should be paid more attention on the evaluation of rubber tree germplasm resources, at the same time the potential impact of other traits on yield also need to be laid some stress on

ANXA6/TRPV2 axis promotes lymphatic metastasis in head and neck squamous cell carcinoma by inducing autophagy

Abstract Background Head and neck squamous cell carcinoma (HNSCC) is highly aggressive with a significant tropism of lymph nodes, which restricts treatment options and negatively impacts patient outcomes. Although progress has been made in understanding the molecular mechanisms underlying lymphatic metastasis (LM), these mechanisms remain elusive. ANXA6 is a scaffold protein that participates in tumor pathogenesis and autophagy regulation; however, how ANXA6 affects autophagy and LM in HNSCC cells remains unknown. Methods RNA sequencing was performed on HNSCC clinical specimens with or without metastasis as well as on The Cancer Genome Atlas dataset to investigate ANXA6 expression and survival. Both in vitro and in vivo studies were performed to investigate the role of ANXA6 in the regulation of LM in HNSCC. The molecular mechanism by which ANXA6 interacts with TRPV2 was examined at the molecular level. Results ANXA6 expression was significantly upregulated in HNSCC patients with LM and higher expression was associated with poor prognosis. ANXA6 overexpression promoted the proliferation and mobility of FaDu and SCC15 cells in vitro; however, ANXA6 knockdown retarded LM in HNSCC in vivo. ANXA6 induced autophagy by inhibiting the AKT/mTOR signaling pathway in HNSCC, thereby regulating the metastatic capability of the disease. Furthermore, ANXA6 expression positively correlated with TRPV2 expression both in vitro and in vivo. Lastly, TRPV2 inhibition reversed ANXA6-induced autophagy and LM. Conclusions These results indicate that the ANXA6/TRPV2 axis facilitates LM in HNSCC by stimulating autophagy. This study provides a theoretical basis for investigating the ANXA6/TRPV2 axis as a potential target for the treatment of HNSCC, as well as a biomarker for predicting LM

HALD, a human aging and longevity knowledge graph for precision gerontology and geroscience analyses

Abstract Human aging is a natural and inevitable biological process that leads to an increased risk of aging-related diseases. Developing anti-aging therapies for aging-related diseases requires a comprehensive understanding of the mechanisms and effects of aging and longevity from a multi-modal and multi-faceted perspective. However, most of the relevant knowledge is scattered in the biomedical literature, the volume of which reached 36 million in PubMed. Here, we presented HALD, a text mining-based human aging and longevity dataset of the biomedical knowledge graph from all published literature related to human aging and longevity in PubMed. HALD integrated multiple state-of-the-art natural language processing (NLP) techniques to improve the accuracy and coverage of the knowledge graph for precision gerontology and geroscience analyses. Up to September 2023, HALD had contained 12,227 entities in 10 types (gene, RNA, protein, carbohydrate, lipid, peptide, pharmaceutical preparations, toxin, mutation, and disease), 115,522 relations, 1,855 aging biomarkers, and 525 longevity biomarkers from 339,918 biomedical articles in PubMed. HALD is available at https://bis.zju.edu.cn/hald

Loss of NFBD1/MDC1 disrupts homologous recombination repair and sensitizes nasopharyngeal carcinoma cells to PARP inhibitors

Abstract Background Nasopharyngeal carcinoma (NPC), a highly invasive tumor, exhibits a distinctive racial and geographic distribution. As options of agents for effective combination chemoradiotherapy for advanced NPC are limited, novel therapeutic approaches are desperately needed. Here the potential of silencing NFBD1 in combination with PARP inhibition as a novel therapeutic strategy for NPC was investigated. Methods To investigate the function of NFBD1, we created NFBD1-depleted NPC cell lines via lentivirus mediated shRNA, and the colony formation, MTS assay, comet assay and apoptosis analysis were used to evaluate the sensitivity of NFBD1 knockdown on PARP inhibition. The signaling change was assessed by western blot, Immunofluorescence and flow cytometry. Furthermore, Xenografts model was used to evaluate the role of silencing NFBD1 in combination with PARP inhibition. Results We find that silencing NFBD1 in combination with PARP inhibition significantly inhibits the cell proliferation and cell cycle checkpoint activity, and increases the apoptosis and DNA damage. Mechanistic studies reveal that NFBD1 loss blocks olaparib-induced homologous recombination repair by decreasing the formation of BRCA1, BRCA2 and RAD51 foci. Furthermore, the xenograft tumor model demonstrated significantly increases sensitivity towards PARP inhibition under NFBD1 deficiency. Conclusions We show that NFBD1 depletion may possess sensitizing effects of PARP inhibitor, and consequently offers novel therapeutic options for a significant subset of patients

Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition

Abstract Background The endothelial-to-hematopoietic transition (EHT) process during definitive hematopoiesis is highly conserved in vertebrates. Stage-specific expression of transposable elements (TEs) has been detected during zebrafish EHT and may promote hematopoietic stem cell (HSC) formation by activating inflammatory signaling. However, little is known about how TEs contribute to the EHT process in human and mouse. Results We reconstructed the single-cell EHT trajectories of human and mouse and resolved the dynamic expression patterns of TEs during EHT. Most TEs presented a transient co-upregulation pattern along the conserved EHT trajectories, coinciding with the temporal relaxation of epigenetic silencing systems. TE products can be sensed by multiple pattern recognition receptors, triggering inflammatory signaling to facilitate HSC emergence. Interestingly, we observed that hypoxia-related signals were enriched in cells with higher TE expression. Furthermore, we constructed the hematopoietic cis-regulatory network of accessible TEs and identified potential TE-derived enhancers that may boost the expression of specific EHT marker genes. Conclusions Our study provides a systematic vision of how TEs are dynamically controlled to promote the hematopoietic fate decisions through transcriptional and cis-regulatory networks, and pre-train the immunity of nascent HSCs

<i>HbCBF1</i> overexpression in <i>Arabidopsis</i>.

<p>(A) Southern blotting of <i>HbCBF1</i> in transgenic plants. (B) <i>HbCBF1</i> expression in OE-3, OE-6 and OE-13 lines. The gene expression was detected by Northern blotting analysis using the <i>HbCBF1</i> probe. (C) Thirty days old seedlings of <i>col-0</i>, OE-3, OE-6 and OE-13 lines showed decreased plant height.</p

Functional Characterization of <i>Hevea brasiliensis CRT/DRE Binding Factor 1</i> Gene Revealed Regulation Potential in the CBF Pathway of Tropical Perennial Tree

<div><p>Rubber trees (<i>Hevea brasiliensis</i>) are susceptible to low temperature and therefore are only planted in the tropical regions. In the past few decades, although rubber trees have been successfully planted in the northern margin of tropical area in China, they suffered from cold injury during the winter. To understand the physiological response under cold stress, we isolated a C-repeat binding factor 1 (<i>CBF1</i>) gene from the rubber tree. This gene (<i>HbCBF1)</i> was found to respond to cold stress but not drought or ABA stress. The corresponding HbCBF1 protein showed CRT/DRE binding activity in gel shift experiment. To further characterize its molecular function, the <i>HbCBF1</i> gene was overexpressed in <i>Arabidopsis</i>. The <i>HbCBF1</i> over expression (OE) line showed enhanced cold resistance and relatively slow dehydration, and the expression of <i>Arabidopsis</i> CBF pathway downstream target genes, e.g. <i>AtCOR15a</i> and <i>AtRD29a</i>, were significantly activated under non-acclimation condition. These data suggest <i>HbCBF1</i> gene is a functional member of the CBF gene family, and may play important regulation function in rubber tree.</p></div

Gel mobility shift assay of recombinant HbCBF1 protein indicated CRT/DRE binding activity.

<p><b>(A)</b> Probes sequences used in this analysis. Bolded nucleotides are CRT/DRE motif, while underlined nucleotides are the mutation sites. <b>(B)</b> HbCBF1 bound with CRT/DRE elements specifically <i>in vitro</i>. Four microgram total proteins of GST (lane 1 from the left) or GST::HbCBF1 (lane 2–9 from the left) were used for the binding with labeled hot COR15a probe. One hundred and twenty-five folds molar unlabelled cold competitor probes were added as indicated (labe 3–9 from the left) in each reactions. The retarded binding bands and free non-binding probe were indicated as "B" and "F" respectively.</p

<i>HbCBF1</i> overexpression conferred cold resistance and relatively slow dehydration in <i>Arabidopsis</i>.

<p>(A) The electrolyte leakage rates of <i>col-0</i>, OE-3, OE-6 and OE-13 lines under nonacclimated (warm) or 5-days cold—acclimated conditions (cold). Electrolyte leakage was measured using leaves from two-week-old seedlings frozen to -7°C at a refrigerating rate of 1°C per h from -1°C. The star symbol (*) indicates significant difference between each individual OE line and wild type plants (WT). (B) Representative seedlings of <i>col-0</i>, OE-3, OE-6 and OE-13 lines recovered from 18 hours frozen at -6°C. The survival rates of each line were listed. (C) The dehydration rates of the detached leaves from <i>col-0</i>, OE-3, OE-6 and OE-13 seedlings. The star (*) symbol indicates significant difference between WT and each individual OE line, while plus symbols (+) shows significant difference between WT and individual OE-6 and OE-13 line. Data in A and C were presented as mean ± standard error of mean of five biological replicates. Significance was determined by Student’s <i>t</i> test at the probability levels of <i>P</i> < 0.05. Comparisons were made between the wild type plant and each individual overexpressing line. For B, totally thirty to fifty plants were tested for each line and about ten seedlings were grown in each pot.</p