The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis

Background Manchurian walnut (Juglans mandshurica Maxim.) is a tree with multiple industrial uses and medicinal properties in the Juglandaceae family (walnuts and hickories). J. mandshurica produces juglone, which is a toxic allelopathic agent and has potential utilization value. Furthermore, the seed of J. mandshurica is rich in various unsaturated fatty acids and has high nutritive value. Findings Here, we present a high-quality chromosome-scale reference genome assembly and annotation for J. mandshurica (n = 16) with a contig N50 of 21.4 Mb by combining PacBio high-fidelity reads with high-throughput chromosome conformation capture data. The assembled genome has an estimated sequence size of 548.7 Mb and consists of 657 contigs, 623 scaffolds, and 40,453 protein-coding genes. In total, 60.99% of the assembled genome consists of repetitive sequences. Sixteen super-scaffolds corresponding to the 16 chromosomes were assembled, with a scaffold N50 length of 33.7 Mb and a BUSCO complete gene percentage of 98.3%. J. mandshurica displays a close sequence relationship with Juglans cathayensis, with a divergence time of 13.8 million years ago. Combining the high-quality genome, transcriptome, and metabolomics data, we constructed a gene-to-metabolite network and identified 566 core and conserved differentially expressed genes, which may be involved in juglone biosynthesis. Five CYP450 genes were found that may contribute to juglone accumulation. NAC, bZip, NF-YA, and NF-YC are positively correlated with the juglone content. Some candidate regulators (e.g., FUS3, ABI3, LEC2, and WRI1 transcription factors) involved in the regulation of lipid biosynthesis were also identified. Conclusions Our genomic data provide new insights into the evolution of the walnut genome and create a new platform for accelerating molecular breeding and improving the comprehensive utilization of these economically important tree species

DOTA: A Double Truthful Auction for Spectrum Allocation in Dynamic Spectrum Access

Abstract—Spectrum auctions have been proposed as an effective approach to fairly and efficiently trade the scarce spectrum resource among wireless users. The most significant challenge of the auction design to provide economic robustness, particularly truthfulness, under the local-dependent interference constraints. However, existing designs either do not consider spectrum reuse or are based on the impractical assumption that each user requests at most one channel. In this paper, we address this problem by proposing DOTA, a DOuble Truthful Auction for dynamic spectrum access. DOTA is economic-robust in terms of truthfulness, individual rationality, and no-deficit. It achieves improved utilization by exploiting spectrum reuse as well as dealing with the interference constraints. Moreover, DOTA minimizes the network transaction overhead and provides flexible channel bidding including range bidding and strict bidding. I

Genetic Improvement in Juglans mandshurica and Its Uses in China: Current Status and Future Prospects

Juglans mandshurica is an economically and ecologically valuable species that is used for various construction purposes, making luxurious furniture, as food and sources of medicinal substances and landscaping because of its excellent wood, edible fruits and rich in various types of chemical compounds. In the past few decades, several genetic improvements of J. mandshurica were made, with a focus on the selection of improved varieties and on breeding technology. Many elite provenances and families were selected based on growth traits or wood properties. In recent years, with the increasing demand for high-quality seedlings in Chinese forestry production, the breeding goals of genetic improvement for J. mandshurica were redefined to include other traits, such as fruit yield and contents of medicinal component. However, the improvement processes were still slow due to the long breeding cycle and the limited use of advanced breeding technologies, resulting in the selection of fewer improved varieties. In this review, we summarized the research progresses on genetic improvements of J. mandshurica and other related works, and discussed research gaps and suggested future directions for genetic improvement of the species. The review provides valuable insight for the selection of improved varieties and production of excellent germplasms

Peptide encoded by lncRNA BVES-AS1 promotes cell viability, migration, and invasion in colorectal cancer cells via the SRC/mTOR signaling pathway

Long non-coding RNAs (lncRNAs) have been revealed to harbor open reading frames (ORFs) that can be translated into small peptides. The peptides may participate in the pathogenesis of colorectal cancer (CRC). Herein, we investigated the role of a lncRNA BVES-AS1-encoded peptide in colorectal tumorigenesis. Through bioinformatic analysis, lncRNA BVES-AS1 was predicted to have encoding potential and to be associated with poor prognosis of patients with CRC. In CRC cells, BVES-AS1 was validated to encode a 50-aa-length micro-peptide, named BVES-AS1-201-50aa, through a western blotting method. BVES-AS1-201-50aa enhanced cell viability and promoted the migratory and invasive capacities of HCT116 and SW480 CRC cells in vitro, validated via CCK-8 assay and transwell assay, respectively. Immunofluorescence assay showed that BVES-AS1-201-50aa increased the expression of proliferating cell nuclear antigen (PCNA) and matrix metalloproteinase 9 (MMP9) in CRC cells. We further verified that BVES-AS1-201-50aa targeted and activated the Src/mTOR signaling pathway in CRC cells by co-immunoprecipitation (Co-IP) experiment, qualitative proteomic analysis, and western blotting. Our findings demonstrated that BVES-AS1 could encode a micro-peptide, which promoted CRC cell viability, migration, and invasion in vitro. Our current work broadens the diversity and breadth of lncRNAs in human carcinogenesis

Acupuncture treatment on the motor area of the scalp for motor dysfunction in patients with ischemic stroke: study protocol for a randomized controlled trial

Abstract Background Scalp acupuncture has shown a remarkable treatment efficacy on motor dysfunction in patients with stroke in China, especially the motor area of Jiao’s scalp acupuncture, which is the most widely used treatment. However, previous studies have summarized that the clinical curative effect of acupuncture treatment for stroke remains uncertain. Meanwhile, no randomized controlled trials on Jiao’s scalp acupuncture have been performed. The aim of this study is to evaluate the efficacy and safety of Jiao’s scalp acupuncture for motor dysfunction in ischemic stroke. Methods/design This is an assessor- and analyst-blinded, randomized controlled trial. One hundred and eight stroke patients with motor dysfunction meeting the inclusion criteria will be allocated by a 1:1 ratio into either an acupuncture treatment group or a control group. Stroke patients in the control group will receive conventional rehabilitation treatment, whereas a combination of Jiao’s scalp acupuncture and conventional rehabilitation treatment will be applied to the acupuncture group. Forty treatment sessions will be performed over an 8-week period. The Fugl-Meyer Assessment scale will be assessed as the primary outcome measure. The Modified Barthel Index, the Stroke-Specific Quality of Life, and the Stroke Syndrome of Traditional Chinese Medicine scales will be selected as secondary outcome measurements. All assessments will be conducted at baseline, week 4 (treatment 20), week 8 (treatment 40), week 12 (follow-up), and week 16 (follow-up). Discussion This is the first trial evaluating the efficacy and safety of Jiao’s scalp acupuncture for motor dysfunction in ischemic stroke. The results of this trial are expected to provide relevant evidence demonstrating that Jiao’s scalp acupuncture can be used as an effective rehabilitation treatment method for improving motor dysfunction in ischemic stroke. Trial registration ClinicalTrials.gov, NCT02871453 . Registered on 17 July 2016

Radiation enhances the invasive potential of primary glioblastoma cells via activation of the Rho signaling pathway.

Glioblastoma multiforme (GBM) is among the most treatment-refractory of all human tumors. Radiation is effective at prolonging survival of GBM patients; however, the vast majority of GBM patients demonstrate progression at or near the site of original treatment. We have identified primary GBM cell lines that demonstrate increased invasive potential upon radiation exposure. As this represents a novel mechanism by which radiation-treated GBMs can fail therapy, we further investigated the identity of downstream signaling molecules that enhance the invasive phenotype of irradiated GBMs. Matrigel matrices were used to compare the extent of invasion of irradiated vs. non-irradiated GBM cell lines UN3 and GM2. The in vitro invasive potential of these irradiated cells were characterized in the presence of both pharmacologic and dominant negative inhibitors of extracellular matrix and cell signaling molecules including MMP, uPA, IGFR, EGFR, PI-3K, AKT, and Rho kinase. The effect of radiation on the expression of these signaling molecules was determined with Western blot assays. Ultimately, the in vitro tumor invasion results were confirmed using an in vivo 9L GBM model in rats. Using the primary GBM cell lines UN3 and GM2, we found that radiation enhances the invasive potential of these cells via activation of EGFR and IGFR1. Our findings suggest that activation of Rho signaling via PI-3K is required for radiation-induced invasion, although not required for invasion under physiologic conditions. This report clearly demonstrates that radiation-mediated invasion is fundamentally distinct from invasion under normal cellular physiology and identifies potential therapeutic targets to overcome this phenomenon

Survivin enhances radiation resistance in primary human glioblastoma cells via caspase-independent mechanisms.

The observed radioresistance of human glioblastoma multiforme (GBM) poses a major challenge, which, if overcome, may lead to significant advances in the management of this patient population. There is accumulating evidence from correlative studies that Survivin expression is associated with increased malignant potential of human gliomas. The purpose of this study was to investigate whether Survivin plays a direct role in mediating radiation resistance in primary human glioma cell lines, and, if so, investigating the underlying mechanisms. Our panel of GBM cell lines included two that were relatively radiation resistant (GM20 and GM21) and two that were more radiation sensitive (GM22 and GM23), which demonstrated differential levels of Survivin expression between the two groups. Through the use of adenoviral vectors containing either dominant-negative (pAd-S(T34A)) or wild-type Suvrivin (pAd-S(WT)), we were able to inactivate or overexpress Survivin, respectively. Our findings suggest that Survivin plays a critical role in mediating radiation resistance in primary GBM cells, in part through suppression of apoptotic cell death via a caspase-independent manner. We have identified novel mechanisms by which Survivin may enhance tumor cell survival upon radiation exposure such as regulation of double-strand DNA break repair and tumor cell metabolism, which were most evident in the radiation-resistant cell lines. These differences in Survivin function both in radiation-resistant vs radiation-sensitive cell lines and in the presence vs absence of radiation exposure warrant further investigation and highlight potentially important mechanisms of radiation resistance in these tumors

Additional file 1: of Acupuncture treatment on the motor area of the scalp for motor dysfunction in patients with ischemic stroke: study protocol for a randomized controlled trial

SPIRIT checklist. (DOC 127 kb

RTEF-1, an Upstream Gene of Hypoxia-inducible Factor-1α, Accelerates Recovery from Ischemia*

The amount of available hypoxia-inducible factor (HIF)-1α has been considered to be largely a consequence of post-translational modification by multiple ubiquitin-proteasome pathways. However, the role of transcriptional regulation of HIF-1α is less certain, and the mechanisms of transcriptional regulation of HIF-1α require further investigation. Here we report that related transcriptional enhancer factor-1 (RTEF-1), a member of the TEF transcriptional factor family, transcriptionally regulates the HIF-1α gene under normoxic and hypoxic conditions. The expression of HIF-1α mRNA was decreased in endothelial cells in which RTEF-1 was knocked down with siRNA. Sequential deletional analysis of the HIF-1α promoter revealed that the MCAT-like element in the HIF-1α promoter was essential for HIF-1α transcription. Binding of RTEF-1 to the MCAT-like element was confirmed by ChIP. Treatment of endothelial cells with a HIF-1 inhibitor resulted in retardation of RTEF-1-induced proliferation and tube formation. Moreover, increased HIF-1α expression was observed in transgenic mice expressing RTEF-1 under the VE-cadherin promoter (VE-Cad/RTEF-1). VE-Cad/RTEF-1 mice subjected to hindlimb ischemia demonstrated increased levels of HIF-1α, accelerated recovery of blood flow, and increased capillary density compared with littermate controls. These results identify RTEF-1 as a regulator of HIF-1α transcription, which results in up-regulation of HIF-1α and acceleration of recovery from ischemia