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Objective: To evaluate the impact of the residual setup errors from differently shaped region of interest (ROI) and investigate if surface-guided setup can be used in radiotherapy with concurrent tumor treating fields (TTFields) for glioblastoma. Methods: Fifteen patients undergone glioblastoma radiotherapy with concurrent TTFields were involved. Firstly, four shapes of region of interest (ROI) (strip-shaped, T-shaped, ⊥ -shaped and cross-shaped) with medium size relative to the whole face were defined dedicate for patients wearing TTFields transducer arrays. Then, ROI-shape-dependent residual setup errors in six degrees were evaluated using an anthropomorphic head and neck phantom taking CBCT data as reference. Finally, the four types of residual setup errors were converted into corresponding dosimetry deviations (including the target coverage and the organ at risk sparing) of the fifteen radiotherapy plans using a feasible and robust geometric-transform-based method. Results: The algebraic sum of the average residual setup errors in six degrees (mm in translational directions and ° in rotational directions) of the four types were 6.9, 1.1, 4.1 and 3.5 respectively. In terms of the ROI-shape-dependent dosimetry deviations, the D98% of PTV dropped off by (3.4 ± 2.0)% (p < 0.05), (0.3 ± 0.5)% (p < 0.05), (0.9 ± 0.9)% (p < 0.05) and (1.1 ± 0.8)% (p < 0.05). The D98% of CTV dropped off by (0.5 ± 0.6)% (p < 0.05) for the strip-shaped ROI while remained unchanged for others. Conclusion: Surface-guided setup is feasible in radiotherapy with concurrent TTFields and a medium-sized T-shaped ROI is appropriate for the surface-based guidance. [ABSTRACT FROM AUTHOR]

Pinus yunnanensis Franch., one of the pioneer species of wild mountain afforestation in southwest China, plays an essential role in the economy, society and environment of Yunnan Province. Nonetheless, P. yunnanensis' trunk twisting and bending phenomenon has become more common, which significantly restricts its use and economic benefits. In order to clarify the compositional differences between the straight and twisted trunk types of P. yunnanensis and to investigate the reasons for the formation of twisted stems, the present study was carried out to dissect the macroscopic and microscopic structure of the straight and twisted trunk types of P. yunnanensis, to determine the content of cell wall components (lignin, cellulose, hemicellulose), determine the content of endogenous hormones, and the expression validation of phytohormone-related differential genes (GA2OX, COI1, COI2) and cell wall-related genes (XTH16, TCH4). The results showed that the annual rings of twisted trunk types were unevenly distributed, eccentric growth, insignificant decomposition of early and late wood, rounding and widening of the tracheid cells, thickening of the cell wall, and reduction of the cavity diameter; the lignin and hemicellulose contents of twisted trunk types were higher; in twisted trunk types, the contents of gibberellin (GA) and jasmonic acid (JA) increased, and the content of auxin (IAA) was reduced; the GA2OX were significantly down-regulated in twisted trunk types, and the expressions of the genes associated with the cell wall, COI1, COI2, TCH4 and XTH16, were significantly up-regulated. In conclusion, the present study found that the uneven distribution of endogenous hormones may be an important factor leading to the formation of twisted trunk type of P. yunnanensis, which adds new discoveries to reveal the mechanism of the genesis of different trunk types in plants, and provides a theoretical basis for the genetic improvement of forest trees. [ABSTRACT FROM AUTHOR]

Nasopharyngeal carcinoma (NPC) has a unique geographic distribution. It is unknown whether meteorological factors are related to the incidence of NPC. To investigate the effect of ambient temperature, relative humidity (RH), and absolute humidity (AH) on the incidence of NPC, we collected the incidence rate of NPC in 2016 and meteorological data from 2006 to 2016 from 484 cities and counties across 31 provinces in China. Generalized additive models with quasi‐Poisson regression and generalized linear models with natural cubic splines were employed respectively to elucidate the nonlinear relationships and specify the partial linear relationships. Subgroup and interactive analysis were also conducted. Temperature (R2 = 0.68, p <.001), RH (R2 = 0.47, p <.001), and AH (R2 = 0.70, p <.001) exhibited nonlinear correlations with NPC incidence rate. The risk of NPC incidence increased by 20.3% (95% confidence intervals [CI]: [18.9%, 21.7%]) per 1°C increase in temperature, by 6.3% (95% CI: [5.3%, 7.2%]) per 1% increase in RH, and by 32.2% (95% CI: [30.7%, 33.7%]) per 1 g/m3 increase in AH, between their the 25th and the 99th percentiles. In addition, the combination of low temperature and low RH was also related to increased risk (relative risk: 1.60, 95% CI: [1.18, 2.17]). Males and eastern or rural populations tended to be more vulnerable. In summary, this study suggests that ambient temperature, RH, and particularly AH are associated with the risk of NPC incidence. [ABSTRACT FROM AUTHOR]

The plant homeodomain finger (PHD finger) protein, a type of zinc finger protein extensively distributed in eukaryotes, plays diverse roles in regulating plant growth and development. While PHD finger proteins have been identified in various species, their functions remain largely unexplored in pea (Pisum sativum). In this study, we identified 84 members of the PHD finger gene family in pea, which displayed an uneven distribution across seven chromosomes. Through a comprehensive analysis using data from Arabidopsis thaliana and Medicago truncatula, we categorized the PHD finger proteins into 20 subfamilies via phylogenetic tree analysis. Each subfamily exhibited distinct variations in terms of quantity, genetic structure, conserved domains, and physical and chemical properties. Collinearity analysis revealed conserved evolutionary relationships among the PHD finger genes across the three different species. Furthermore, we identified the conserved and important roles of the subfamily M members in anther development. RT-qPCR and in situ hybridization revealed high expression of the pea subfamily M members PsPHD11 and PsPHD16 in microspores and the tapetum layer. In conclusion, this analysis of the PHD finger family in pea provides valuable guidance for future research on the biological roles of PHD finger proteins in pea and other leguminous plants. [ABSTRACT FROM AUTHOR]

DNA methylation is an important mechanism for epigenetic modifications that have been shown to be associated with responses to plant development. Previous studies found that inverted Populus yunnanensis cuttings were still viable and could develop into complete plants. However, the growth status of inverted cuttings was weaker than that of upright cuttings, and the sprouting time of inverted cuttings was later than that of upright cuttings. There is currently no research on DNA methylation patterns in inverted cuttings of Populus yunnanensis. In this study, we detected genome-wide methylation patterns of stem tips of Populus yunnanensis at the early growth stage and the rapid growth stage by Oxford Nanopore Technologies (ONT) methylation sequencing. We found that the methylation levels of CpG, CHG, CHH, and 6mA were 41.34%, 33.79%, 17.27%, and 12.90%, respectively, in the genome of inverted poplar cuttings, while the methylation levels of the four methylation types were higher in the genome of upright poplar cuttings than in inverted cuttings, 41.90%, 34.57%, 18.09%, and 14.11%, suggesting important roles for DNA methylation in poplar cells. In all comparison groups, CpG-type methylation genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were annotated to pathways associated with carbon metabolism, ribosome biogenesis in eukaryotes, glycolysis/gluconeogenesis, pyruvate metabolism, and mRNA detection pathways, suggesting that different biological processes are activated in upright and inverted cuttings. The results show that methylation genes are commonly present in the poplar genome, but only a few of them are involved in the regulation of expression in the growth and development of inverted cuttings. From this, we screened the DET2 gene for significant differences in methylation levels in upright or inverted cuttings. The DET2 gene is a key gene in the Brassinolide (BRs) synthesis pathway, and BRs have an important influence on the growth and development process of plants. These results provide important clues for studying DNA methylation patterns in P. yunnanensis. [ABSTRACT FROM AUTHOR]

Introduction: Although esophageal bronchogenic cysts are benign diseases, they may be accompanied by serious complications and have the possibility of recurrence. Therefore, once confirmed, it is necessary to treat the esophagobronchial cyst when the contraindication is excluded. Endoscopic treatment is usually used for lesions with small diameter and shallow origin, and has the advantages of small surgical trauma and risk, which can reduce the psychological burden of patients to a certain extent, help them to recover quickly, and lower hospital costs. Case presentation: Case 1 is a 54-year-old Han Chinese man admitted to our hospital who complained of difficulty swallowing in the past 6 months. Case 2 is a 41-year-old Han Chinese man who was hospitalized in the past 3 months due to chest discomfort. Endoscopic ultrasound revealed a hypoechoic cystic lesion arising from the muscularis propria. Submucosal tunneling endoscopic resection was performed using a dual knife, and a cystic mass was observed between the mucosa and the muscular layers of the esophagus. On locating the cyst, an incision was made on the oral side of the lesion for evacuation. The cyst wall was excised using endoscopic argon plasma coagulation. We successfully removed the esophageal bronchogenic cyst lesion in the intrinsic muscle layer using submucosal tunneling endoscopic resection. Conclusion: Esophageal bronchogenic cysts are rare in clinical practice and lack specificity in clinical manifestations. Multiple methods can be used to determine the location and nature of the lesion and ultimately determine the treatment plan. Surgical resection and endoscopic treatment are two different treatment methods, and appropriate treatment plans need to be selected on the basis of the origin layer, size, and relationship with the esophagus of the lesion to reduce complications and improve prognosis. [ABSTRACT FROM AUTHOR]

SUMMARY: Rosa roxburghii and Rosa sterilis, two species belonging to the Rosaceae family, are widespread in the southwest of China. These species have gained recognition for their remarkable abundance of ascorbate in their fresh fruits, making them an ideal vitamin C resource. In this study, we generated two high‐quality chromosome‐scale genome assemblies for R. roxburghii and R. sterilis, with genome sizes of 504 and 981.2 Mb, respectively. Notably, we present a haplotype‐resolved, chromosome‐scale assembly for diploid R. sterilis. Our results indicated that R. sterilis originated from the hybridization of R. roxburghii and R. longicuspis. Genome analysis revealed the absence of recent whole‐genome duplications in both species and identified a series of duplicated genes that possibly contributing to the accumulation of flavonoids. We identified two genes in the ascorbate synthesis pathway, GGP and GalLDH, that show signs of positive selection, along with high expression levels of GDP‐d‐mannose 3′, 5′‐epimerase (GME) and GDP‐l‐galactose phosphorylase (GGP) during fruit development. Furthermore, through co‐expression network analysis, we identified key hub genes (MYB5 and bZIP) that likely regulate genes in the ascorbate synthesis pathway, promoting ascorbate biosynthesis. Additionally, we observed the expansion of terpene synthase genes in these two species and tissue expression patterns, suggesting their involvement in terpenoid biosynthesis. Our research provides valuable insights into genome evolution and the molecular basis of the high concentration of ascorbate in these two Rosa species. [ABSTRACT FROM AUTHOR]

(1) Background: Brassinosteroids (BRs) are important hormones involved in almost all stages of plant growth and development, and sterol dehydrogenase is a key enzyme involved in BRs biosynthesis. However, the sterol dehydrogenase gene family of Populus yunnanensis Dode (P. yunnanensis) has not been studied. (2) Methods: The PyDET2 (DEETIOLATED2) gene family was identified and analyzed. Three genes were screened based on RNA-seq of the stem tips, and the PyDET2e was further investigated via qRT-PCR (quantitative real-time polymerase chain reaction) and subcellular localization. (3) Results: The 14 DET2 family genes in P. yunnanensis were categorized into four groups, and 10 conserved protein motifs were identified. The gene structure, chromosome distribution, collinearity, and codon preference of all PyDET2 genes in the P. yunnanensis genome were analyzed. The codon preference of this family is towards the A/U ending, which is strongly influenced by natural selection. The PyDET2e gene was expressed at a higher level in September than in July, and it was significantly expressed in stems, stem tips, and leaves. The PyDET2e protein was localized in chloroplasts. (4) Conclusions: The PyDET2e plays an important role in the rapid growth period of P. yunnanensis. This systematic analysis provides a basis for the genome-wide identification of genes related to the brassinolide biosynthesis process in P. yunnanensis, and lays a foundation for the study of the rapid growth mechanism of P. yunnanensis. [ABSTRACT FROM AUTHOR]

Ionizing radiation (IR) induces ferroptosis in head and neck squamous cell carcinoma (HNSCC). But, it remains unclear whether ferroptosis affects the prognosis of HNSCC patients after receiving radiotherapy. This study aims to develop a ferroptosis signature to predict the radiosensitivity and prognosis of HNSCC. Ferroptosis-related genes, clinical data and RNA expression profiles were obtained from the FerrDb database, The Cancer Genome Atlas and GEO database. Prognostic genes were identified by random survival forest, univariate Cox regression, Kaplan–Meier and ROC analyses. Principal component analysis, multivariate Cox regression, nomogram and DCA analyses were conducted to estimate its predictive ability. Functional enrichment and immune-related analyses were performed to explore potential biological mechanisms and tumor immune microenvironment. The effect of the hub gene on ferroptosis and radiosensitivity was verified using flow cytometry, quantitative real-time PCR and clonogenic survival assay. We constructed a ferroptosis-related signature, including IL6, NCF2, metadherin (MTDH) and CBS. We classified patients into high-risk (HRisk) and low-risk groups according to the risk scores. The risk score was confirmed to be an independent predictor for overall survival (OS). Combining the clinical stage with the risk score, we established a predictive nomogram for OS. Furthermore, pathways related to tumorigenesis and tumor immune suppression were mainly enriched in HRisk. MTDH was verified to have a potent effect on IR-induced ferroptosis and consequently promoted radiosensitivity. We constructed a ferroptosis-related signature to predict radiosensitivity and OS in HNSCC patients. MTDH was identified as a promising therapeutic target in radioresistant HNSCC patients. [ABSTRACT FROM AUTHOR]

Having a spiral grain is considered to be one of the most important wood properties influencing wood quality. Here, transcriptome profiles and metabolome data were analyzed in the straight grain and twist grain of Pinus yunnanensis. A total of 6644 differential expression genes were found between the straight type and the twist type. A total of 126 differentially accumulated metabolites were detected. There were 24 common differential pathways identified from the transcriptome and metabolome, and these pathways were mainly annotated in ABC transporters, arginine and proline metabolism, flavonoid biosynthesis, isoquinoline alkaloid biosynthesis, linoleic acid metabolism, phenylpropanoid, tryptophan metabolism, etc. A weighted gene coexpression network analysis showed that the lightblue4 module was significantly correlated with 2′-deoxyuridine and that transcription factors (basic leucine zipper (bZIP), homeodomain leucine zipper (HD-ZIP), basic helix–loop–helix (bHLH), p-coumarate 3-hydroxylase (C3H), and N-acetylcysteine (NAC)) play important roles in regulating 2′-deoxyuridine, which may be involved in the formation of spiral grains. Meanwhile, the signal transduction of hormones may be related to spiral grain, as previously reported. ARF7 and MKK4_5, as indoleacetic acid (IAA)- and ethylene (ET)-related receptors, may explain the contribution of plant hormones in spiral grain. This study provided useful information on spiral grain in P. yunnanensis by transcriptome and metabolome analyses and could lay the foundation for future molecular breeding. [ABSTRACT FROM AUTHOR]

Background: Super enhancers (SE) play pivotal roles in cell identity and diseases occur including tumorigenesis. The depletion of SE‐associated lncRNA transcripts, also known as super‐lncRNA, causes the activity of SE to be dysregulated. Methods: We screened and identified an elevated metastasis‐associated SE‐lncRNA SUCLG2‐AS1 in nasopharyngeal carcinoma (NPC) using RNA‐sequencing, real‐time quantitative polymerase chain reaction (RT‐qPCR) and bioinformatics. Western blotting, RT‐qPCR, methylated RNA immunoprecipitation (MeRIP), RNA immunoprecipitation, chromatin immunoprecipitation, RNA pull‐down and 3C (chromosome conformation capture assays) were used for mechanistic studies. Results: SUCLG2‐AS1 was correlated with a poor prognosis. SUCLG2‐AS1 promotes NPC cell invasion and metastasis while repressing apoptosis and radiosensitivity in vitro and in vivo. Mechanistically, high SUCLG2‐AS1 expression occurred in an m6A‐dependent manner. SUCLG2‐AS1 was found to be located in the SE region of SOX2, and it regulated the expression of SOX2 via long‐range chromatin loop formation, which via mediating CTCF (transcription factor) occupied the SE and promoter region of SOX2, thus regulating the metastasis and radiosensitivity of NPC. Conclusions: Taken together, our data suggest that SUCLG2‐AS1 may serve as a novel intervention target for the clinical treatment of NPC. [ABSTRACT FROM AUTHOR]

The long non‐coding RNA (lncRNA)–microRNA (miRNA) interaction network plays a crucial part in the pathogenesis of nasopharyngeal carcinoma (NPC). Here, we discovered a relationship between LINC01376 and miR‐4757 in NPC tumor development. First, LINC01376 was abnormally overexpressed in NPC tissues and cells, and its elevated expression was associated with advanced clinical stage and shorter distant metastasis‐free survival time. Moreover, biological experiments showed that LINC01376 facilitated the proliferative, invasive, and migratory abilities of NPC cells in vitro and in vivo. Mechanistically, bioinformatics and RT‐qPCR assays revealed that LINC01376 knockdown upregulated the expression level of downstream miR‐4757, including miR‐4757 primary transcript (pri‐miR‐4757) and mature miR‐4757. Furthermore, LINC01376 competitively sponged the transcription factor SP1 and reduced its enrichment in the upstream promoter region of miR‐4757 to repress miR‐4757 expression. Finally, insulin‐like growth factor 1(IGF1) was identified as the target of miR‐4757. Rescue experiments indicated that LINC01376 accelerated NPC cell proliferation, migration, and invasion through the miR‐4757‐5p/IGF1 axis. In conclusion, the SP1/miR‐4757/IGF1 axis, which is regulated by LINC01376 in NPC deterioration and metastasis, is expected to provide new insights into the molecular mechanism of NPC carcinogenesis. [ABSTRACT FROM AUTHOR]

MYB transcriptional regulators belong to one of the most significant transcription factors families in plants, among which R2R3‐MYB transcription factors are involved in plant growth and development, hormone signal transduction, and stress response. Two R2R3‐MYB transcription factors, FLP and its paralogous AtMYB88, redundantly regulate the symmetrical division of guard mother cells (GMCs), and abiotic stress response in Arabidopsis thaliana. Only one orthologue gene of FLP was identified in pea (Pisum sativum FLP; PsFLP). In this study, we explored the gene function of PsFLP by virus‐induced gene silencing (VIGS) technology. The phenotypic analysis displayed that the silencing of PsFLP expression led to the abnormal development of stomata and the emergence of multiple guard cells tightly united. In addition, the abnormal stomata of flp could be fully rescued by PsFLP driven by the FLP promoter. In conclusion, the results showed that PsFLP plays a conservative negative role in regulating the symmetric division of GMC during stomatal development. Based on real‐time quantitative PCR, the relative expressions of AAO3, NCED3, and SnRK2.3 significantly increased in the flp pFLP::PsFLP plants compared to mutant, indicating that PsFLP might be involved in drought stress response. Thus, PsFLP regulates the genes related to cell cycle division during the stomatal development of peas and participates in response to drought stress. The study provides a basis for further research on its function and application in leguminous crop breeding. [ABSTRACT FROM AUTHOR]

Background: Recurrence due to the development of radioresistance remains a major challenge in the clinical management of nasopharyngeal carcinoma. The objective of this study was to increase the sensitivity of nasopharyngeal carcinoma cells to ionizing radiation by enhancing oxidative stress and ferroptosis caused by disrupting the mitochondrial anti-oxidant enzyme system. Methods: Oxidative stress cell model was constructed by SOD2 knockdown using shRNA. The expression and activity of DHODH was suppressed by siRNA and brequinar in SOD2 depleted cells. Protein levels were determined by western blotting and ferroptosis was assessed by C11 BODIPY and malondialdehyde assay. Cell viability was evaluated using CCK-8 assay while radiotoxicity was assessed by colony formation assay. Cellular ATP level was determined by ATP assay kits, ROS was determined by DCFD and DHE, while mitochondrial oxygen consumption was determined by seahorse assay. Data were analyzed by two-tailed independent t-test. Results: Radiation upregulated SOD2 expression and SOD2 depletion increased cellular O2.−, malondialdehyde, and the fluorescence intensity of oxidized C11 BODIPY. It also resulted in mitochondrial damage. Its depletion decreased colony formation both under ionizing and non-ionizing radiation conditions. The ferroptosis inhibitor, deferoxamine, rescued cell viability and colony formation in SOD2 depleted cells. Cellular level of malondialdehyde, fluorescence intensity of oxidized C11 BODIPY, O2.− level, ATP, and mitochondrial oxygen consumption decreased following DHODH inhibition in SOD2 depleted cells. Cell viability and colony formation was rescued by DHODH inhibition in SOD2 depleted cells. Conclusion: Inducing oxidative stress by SOD2 inhibition sensitized nasopharyngeal carcinoma cells to ionizing radiation via ferroptosis induction. This was found to be dependent on DHODH activity. This suggests that DHODH inhibitors should be used with caution during radiotherapy in nasopharyngeal carcinoma patients. [ABSTRACT FROM AUTHOR]

(1) Background: Lignin is a unique component of the secondary cell wall, which provides structural support for perennial woody plants. ARFs are the core factors of the auxin-signaling pathway, which plays an important role in promoting plant growth, but the specific relationship between auxin response factors (ARFs) and lignin has not been fully elucidated with regard to rapid plant growth in forest trees. (2) Objectives: This study aimed to investigate the relationship between ARFs and lignin with regard to rapid plant growth in forest trees. (3) Methods: We used bioinformatics analysis to investigate the PyuARF family, find genes homologous to ARF6 and ARF8 in Populus yunnanensis, and explore the changes in gene expression and lignin content under light treatment. (4) Results: We identified and characterized 35 PyuARFs based on chromosome-level genome data from P. yunnanensis. In total, we identified 92 ARF genes in P. yunnanensis, Arabidopsis thaliana, and Populus trichocarpa, which were subsequently divided into three subgroups based on phylogenetic analysis and classified the conserved exon–intron structures and motif compositions of the ARFs into the same subgroups. Collinearity analysis suggested that segmental duplication and whole-genome duplication events were majorly responsible for the expansion of the PyuARF family, and the analysis of Ka/Ks indicated that the majority of the duplicated PyuARFs underwent purifying selection. The analysis of cis-acting elements showed that PyuARFs were sensitive to light, plant hormones, and stress. We analyzed the tissue-specific transcription profiles of PyuARFs with transcriptional activation function and the transcription profiles of PyuARFs with high expression under light in the stem. We also measured the lignin content under light treatment. The data showed that the lignin content was lower, and the gene transcription profiles were more limited under red light than under white light on days 1, 7, and 14 of the light treatments. The results suggest that PyuARF16/33 may be involved in the regulation of lignin synthesis, thereby promoting the rapid growth of P. yunnanensis. (5) Conclusions: Collectively, this study firstly reports that PyuARF16/33 may be involved in the regulation of lignin synthesis and in promoting the rapid growth in P. yunnanensis. [ABSTRACT FROM AUTHOR]

Background: Toxicodendron vernicifluum, belonging to the family Anacardiaceae, is an important commercial arbor species, which can provide us with the raw lacquer, an excellent adhesive and painting material used to make lacquer ware. Compared with diploid, triploid lacquer tree has a higher yield of raw lacquer and stronger resistance to stress. Triploid T. vernicifluum was a newly discovered natural triploid lacquer tree. However, the taxonomy of triploid T. vernicifluum has remained uncertain. Here, we sequenced and analyzed the complete chloroplast (cp) genome of triploid T. vernicifluum and compared it with related species of Toxicodendron genus based on chloroplast genome and SSR markers. Results: The plastome of triploid T. vernicifluum is 158,221 bp in length, including a pair of inverted repeats (IRs) of 26,462 bp, separated by a large single-copy region of 86,951 bp and a small single-copy region of 18,346 bp. In total, 132 genes including 87 protein-coding genes, 37 tRNA genes and 8 rRNA genes were identified in the triploid T. vernicifluum. Among these, 16 genes were duplicated in the IR regions, 14 genes contain one intron, while three genes contain two introns. After nucleotide substitutions, seven small inversions were analyzed in the chloroplast genomes, eight hotspot regions were found, which could be useful molecular genetic markers for future population genetics. Phylogenetic analyses showed that triploid T. vernicifluum was a sister to T. vernicifluum cv. Dahongpao and T. vernicifluum cv. Hongpigaobachi. Moreover, phylogenetic clustering based on the SSR markers showed that all the samples of triploid T. vernicifluum, T. vernicifluum cv. Dahongpao and T. vernicifluum cv. Hongpigaobachi in one group, while the samples of T. vernicifluum and T. succedaneum in another group, which is consistent with the cp genome and morphological analysis. Conclusions: The current genomic datasets provide pivotal genetic resources to determine the phylogenetic relationships, variety identification, breeding and resource exploitation, and future genetic diversity-related studies of T. vernicifluum. [ABSTRACT FROM AUTHOR]

(1) Background: Populus yunnanensis Dode (P. yunnanensis) grows in the low-latitude and high-altitude areas of southwest China. In low-latitude and high-altitude areas, plants suffer from the high intensity of UV-B (ultraviolet-b) radiation, and they have a complete regulation system to adapt to the environment of the high UV-B radiation. As natural antioxidants, anthocyanins play an important role in scavenging free radicals. BBX (B-box) genes are involved in anthocyanins biosynthesis. (2) Methods: By exploring the gene structure and motifs of PyunBBX genes (genes of P. yunnanensis BBX family) and the evolutionary relationship between PyunBBX genes and other species BBX genes, six PyunBBX genes that responded to UV-B and participated in anthocyanins biosynthesis were screened. BBX, with the potential to regulate anthocyanins biosynthesis, was further investigated by anthocyanins content determination and RT-qPCR (real-time quantitative polymerase chain reaction); (3) Results: After 7 days of UV-B treatment, anthocyanins were significantly accumulated, and the expression of PyunBBX18 was up-regulated for 7 days. The expression of PyunBBX12 was inhibited by UV-B treatment. By analyzing the RNA-seq data of leaves and bark of P. yunnanensis, we found that PyunBBX18 was highly expressed in leaves and young bark; (4) Conclusions: These results showed that PyunBBX18 and PyunBBX12 may be involved in the response process of UV-B stress, in which PyunBBX18 may regulate the anthocyanins biosynthesis to resist UV damage. [ABSTRACT FROM AUTHOR]

Purpose. Gastric cancer is one of the most common malignancies with high mortality worldwide. It is known that long noncoding RNAs (lncRNAs) play important roles in the pathogenesis of gastric cancer. This study investigates the role of lncRNA ZNF667-AS1 in gastric cancer cells. Methods. We have applied real-time quantitative PCR (qPCR) to study the levels of ZNF667-AS1 in gastric cancer biopsies and cell lines. The effects of ZNF667-AS1 on the propagation, clonogenicity, metastasis, and angiogenesis of gastric cancer cells were evaluated by calorimetry, colony formation, cell migration, and angiogenesis assays. Western blotting was used to identify the levels of proteins involved in cancer invasion and angiogenesis signaling pathways. Result. It was found that lncRNA ZNF667-AS1 was downregulated in gastric cancer biopsies. Overexpression of ZNF667-AS1 reduced the propagation, migration, and angiogenesis of gastric cancer cells. Molecular mechanism studies displayed that the high level of lncRNA ZNF667-AS1 promoted the expression of E-cadherin and inhibited the expression of N-cadherin and VEGFA, leading to the inhibition of the proliferation, migration, and angiogenesis of gastric cancer cells. Conclusion. As a tumor suppressor gene, lncRNA ZNF667-AS1 significantly hinders the propagation, metastasis, and angiogenesis of gastric cancer cells by promoting the expression of E-cadherin and inhibiting the expression of N-cadherin and VEGFA. Therefore, lncRNA ZNF667-AS1 could play a synergistic therapeutic role by targeting tumor cells and vascular endothelial cells, which represents a new therapeutic scheme for novel therapeutics of gastric cancer. [ABSTRACT FROM AUTHOR]

Background: Increasing evidence shows that endothelial apoptosis contributes to cigarette smoke (CS)-induced disease progression, such as chronic obstructive pulmonary disease (COPD). Our previous studies have validated Notch1 as an anti-apoptotic signaling in CS-induced endothelial apoptosis. Resveratrol (RESV) is a naturally occurring polyphenol that exhibits an anti-apoptotic activity in endothelial cells that exposed to many kinds of destructive stimulus. However, the effects of resveratrol on Notch1 signaling in CS-induced endothelial apoptosis have not yet been fully elucidated. Therefore, the aim of this study was to examine whether RESV can protect endothelial cells from CS-induced apoptosis via regulating Notch1 signaling.Methods: Human umbilical vein endothelial cells (HUVECs) were pretreated with RESV for 2 h, followed by cotreatment with 2.5%CSE for 24 h to explore the role of RESV in CSE induced endothelial apoptosis. 3-methyladenine (3-MA) or rapamycin was used to alter autophagic levels. Lentivirus Notch1 intracellular domain (LV-N1ICD), γ-secretase inhibitor (DAPT) and Notch1 siRNA were used to change Notch1 expression. The expression of Notch1, autophagic and apoptotic markers were examined by Western blot and the apoptosis rate was detected by Flow cytometry analysis.Results: Our results showed that activating autophagy reduced CSE-induced endothelial apoptosis, while blocking autophagy promoted cell apoptosis in HUVECs. RESV pretreatment attenuated the CSE-induced endothelial apoptosis and activated Notch1 signaling. RESV pretreatment also increased LC3b-II and Beclin1 production, decreased p62 and mTOR expression. 3-MA treatment inhibited autophagy and aggravated CSE induced apoptosis, while rapamycin promoted autophagy, led to a decrease in cell apoptosis. LV-N1ICD transfection upregulated autophagy and reduced apoptosis. However, this protective effect was abolished by 3-MA treatment. In cells treated with DAPT or Notch1 siRNA, autophagy was decreased, while apoptosis was increased. RESV partly rescued the DAPT or Notch1 siRNA induced apoptosis by activating Notch1 signaling.Conclusion: In HUVECs, RESV attenuates CSE induced endothelial apoptosis by inducing autophagy in a Notch1-dependent manner. [ABSTRACT FROM AUTHOR]

Migraine is a debilitating neurological condition, with a global prevalence rate of 10.68% in men and 18.79% in women. Elucidation of the molecular mechanisms underlying migraines is of great importance for improving the quality of life of patients. The release of the neuropeptide calcitonin gene‐related peptide (CGRP) from trigeminal nerve terminals is involved in the pathogenesis of migraine. Recent studies have shown that up‐regulation of miR‐34a‐5p expression is associated with acute migraine attacks. Here, we investigated whether alteration of the expression of miR‐34a‐5p induces the release of the vasoactive peptide CGRP. We isolated primary rat trigeminal ganglion neurons and performed gain‐ and loss‐of‐function assays to alter the expression level of miR‐34a‐5p. Down‐regulation of miR‐34a‐5p inhibited the expression of interleukin‐1β (IL‐1β)/cyclooxygenase 2 (COX2)/prostaglandin E2 (PGE2), decreased IL‐1β, PGE2 and CGRP release, and up‐regulated the expression of silencing information regulator 1 (SIRT1) in trigeminal ganglion, whereas overexpression of miR‐34a‐5p enhanced the expression of IL‐1β/COX2/PGE2, increased the release of IL‐1β, PGE2 and CGRP, and decreased the expression of SIRT1 in trigeminal ganglion. In addition, overexpression of miR‐34a‐5p induced apoptosis in primary rat trigeminal neurons. In summary, these findings suggest that miR‐34a‐5p up‐regulates the IL‐1β/COX2/PGE2 inflammation pathway, induces apoptosis and enhances release of CGRP via inhibition of SIRT1 expression in trigeminal ganglion neurons; thus, miR‐34a‐5p may have potential as a therapeutic target for the treatment of migraine. [ABSTRACT FROM AUTHOR]

Background: The major clinical obstacle that limits the long‐term benefits of treatment with osimertinib (AZD9291) in patients with epidermal growth factor receptor‐mutant non–small cell lung cancer is the development of acquired resistance. Therefore, effective strategies that can overcome acquired resistance to osimertinib are urgently needed. The authors' current efforts in this direction have identified LBH589 (panobinostat), a clinically used histone deacetylase inhibitor, as a potential agent in overcoming osimertinib resistance. Methods: Cell growth and apoptosis in vitro were evaluated by measuring cell numbers and colony formation and by detecting annexin V‐positive cells and protein cleavage, respectively. Drug effects on tumor growth in vivo were assessed with xenografts in nude mice. Alterations of tested proteins in cells were monitored with Western blot analysis. Gene knockout was achieved using the CRISPR/Cas9 technique. Results: The combination of LBH589 and osimertinib synergistically decreased the survival of different osimertinib‐resistant cell lines, including those harboring C797S mutations, with greater inhibition of cell colony formation and growth. The combination enhanced the induction of apoptosis in osimertinib‐resistant cells. Importantly, the combination effectively inhibited the growth of osimertinib‐resistant xenograft tumors in nude mice. Mechanistically, the combination of LBH589 and osimertinib enhanced the elevation of Bim in osimertinib‐resistant cells. Knockout of Bim in osimertinib‐resistant cells substantially attenuated or abolished apoptosis enhanced by the LBH589 and osimertinib combination. These results collectively support a critical role of Bim elevation in the induction of apoptosis of osimertinib‐resistant cells for this combination. Conclusions: The current findings provide strong preclinical evidence in support of the potential for LBH589 to overcome osimertinib resistance in the clinic. The major clinical obstacle that limits the long‐term benefits of treatment with osimertinib in patients with epidermal growth factor receptor–mutant non–small cell lung cancer is the development of acquired resistance. This study provides strong preclinical evidence in support of the potential for histone deacetylase inhibition to overcome osimertinib resistance in the clinic. [ABSTRACT FROM AUTHOR]

Background: The major clinical obstacle that limits the long-term benefits of treatment with osimertinib (AZD9291) in patients with epidermal growth factor receptor-mutant non-small cell lung cancer is the development of acquired resistance. Therefore, effective strategies that can overcome acquired resistance to osimertinib are urgently needed. The authors' current efforts in this direction have identified LBH589 (panobinostat), a clinically used histone deacetylase inhibitor, as a potential agent in overcoming osimertinib resistance.Methods: Cell growth and apoptosis in vitro were evaluated by measuring cell numbers and colony formation and by detecting annexin V-positive cells and protein cleavage, respectively. Drug effects on tumor growth in vivo were assessed with xenografts in nude mice. Alterations of tested proteins in cells were monitored with Western blot analysis. Gene knockout was achieved using the CRISPR/Cas9 technique.Results: The combination of LBH589 and osimertinib synergistically decreased the survival of different osimertinib-resistant cell lines, including those harboring C797S mutations, with greater inhibition of cell colony formation and growth. The combination enhanced the induction of apoptosis in osimertinib-resistant cells. Importantly, the combination effectively inhibited the growth of osimertinib-resistant xenograft tumors in nude mice. Mechanistically, the combination of LBH589 and osimertinib enhanced the elevation of Bim in osimertinib-resistant cells. Knockout of Bim in osimertinib-resistant cells substantially attenuated or abolished apoptosis enhanced by the LBH589 and osimertinib combination. These results collectively support a critical role of Bim elevation in the induction of apoptosis of osimertinib-resistant cells for this combination.Conclusions: The current findings provide strong preclinical evidence in support of the potential for LBH589 to overcome osimertinib resistance in the clinic. [ABSTRACT FROM AUTHOR]

Background: Droplet digital polymerase chain reaction (ddPCR) is an emerging technology for quantitative cell-free DNA oncology applications. However, a ddPCR assay for the epidermal growth factor receptor (EGFR) p.Thr790Met (T790M) mutation suitable for clinical use remains to be established with analytical and clinical validations.Objective: We aimed to develop and validate a new ddPCR assay to quantify the T790M mutation in plasma for monitoring and predicting the progression of advanced non-small-cell lung cancer (NSCLC).Methods: Specificity of the ddPCR assay was evaluated with genomic DNA samples from healthy individuals. The inter- and intraday variations of the assay were evaluated using mixtures of plasmid DNA containing wild-type EGFR and T790M mutation sequences. We assessed the clinical utility of the T790M assay in a multicenter prospective study in patients with advanced NSCLC receiving tyrosine kinase inhibitor (TKI) treatment by analyzing longitudinal plasma DNA samples.Results: We set the criteria for a positive call when the following conditions were satisfied: (1) T790M mutation frequency > 0.098% (3 standard deviations above the background signal); (2) at least two positive droplets in duplicate ddPCR reactions. Among the 62 patients with advanced NSCLC exhibiting resistance to TKI treatment, 15 had one or more serial plasma samples that tested positive for T790M. T790M mutation was detected in the plasma as early as 205 days (median 95 days) before disease progression, determined by imaging analysis. Plasma T790M concentrations also correlated with intervention after disease progression.Conclusions: We developed a ddPCR assay to quantify the T790M mutation in plasma. Quantification of longitudinal plasma T790M mutation may allow noninvasive assessment of drug resistance and guide follow-up treatment in TKI-treated patients with NSCLC.Trial Registration: Clinical Trials.gov identifier: NCT02804100. [ABSTRACT FROM AUTHOR]

Populus tomentosa, of section Populus, is distributed mainly in northern China. This species has high resistance to many diseases and insects, and it plays key roles in shelterbelts and urban afforestation in northern China. It has long been suspected to be a hybrid, but its parents remain unknown. In the present study, we report four newly sequenced complete cp genomes from section Populus and comparative genomic analyses of these new sequences and three published cp genome sequences. The seven cp genomes ranged from 155,853 bp (P. tremula var. davidiana) to 156,746 bp (P. adenopoda) in length, and their gene orders, gene numbers and GC contents were similar. We analyzed SNPs, indels, SSRs and repeats among the seven cp genomes, and eight small inversions were detected in the ndhC-trnV, rbcL-accD, petA-psbJ, trnW-trnP, rpl16-rps3, trnL-ycf15, ycf15-trnL, and ndhF-trnL intergenic regions. Furthermore, seven divergent regions (trnH-psbA, matK, psbM-psbD, ndhC-trnV, ycf1, ndhF-ccsA and ccsA-ndhD) were found in more highly variable regions. The phylogenetic tree reveals that P. tomentosa is closely related to P. alba and P. alba var. pyramidalis. Hence, P. alba was involved in the formation of P. tomentosa. [ABSTRACT FROM AUTHOR]

Background: ZNF488 acts as an oncogene which promotes cell invasion and endows tumor cells stem cell capacity in nasopharyngeal carcinoma (NPC), but its correlation with clinicopathologic characteristics and patients' survival in NPC remain undefined. Methods: In this study, 158 cases of confirmed NPC were subjected to immunohistochemistry staining for evaluating endogenous expression. Kaplan–Meier method and log-rank test were used to estimate the survival rates. The relationship between ZNF488 and clinicopathological characteristics was statistically calculated by chi-squared test, univariate and multivariate analysis. In addition, adhesion assay, MTT and colony formation assays were performed for measuring adhesion and proliferation capacity. Cell cycle analysis via flow cytometry was conducted to explore cell cycle distribution. Western blot was used to detect pathway protein levels, and the pFAK (Y397) kit was used for focal adhesion kinase (FAK) activation. Results: We demonstrated that high expression of ZNF488 was significantly correlated with locoregional failure (P=0.018) and distant metastasis (P=0.001). Patients with high ZNF488 expression had poorer overall survival (P<0.001), loco-regional recurrence-free survival (P<0.001), distance metastasis-free survival (P<0.001) and progression-free survival (P<0.001) than those with low ZNF488 group. Multivariate analysis showed that ZNF488 expression was an independent prognostic indicator for predicting NPC patients' survival (HR, 3.314; 95% CI, 1.489–7.386; P=0.003). Additionally, ZNF488-induced collagen IV/FAK/AKT to enhance adhesion ability meanwhile led to the upregulation of Cyclin D1 to facilitate cell proliferation through promoting cell cycle progression and inhibition of apoptosis through caspase-independent way. Conclusion: These results reveal that ZNF488, as an independent prognostic indicator, promotes cell adhesion and proliferation through collagen IV/FAK/AKT/Cyclin D1 pathway in NPC. [ABSTRACT FROM AUTHOR]

Populus , a core genus of Salicaceae, plays a significant ecological role as a source of pioneer species in boreal forests. However, interspecific hybridization and high levels of morphological variation among poplars have resulted in great difficulty in classifying species for systematic and comparative evolutionary studies. Here, we present phylogenetic analyses of 24 newly sequenced Populus plastomes and 36 plastomes from GenBank, which represent seven genera of Salicaceae, in combination with a matrix of eighteen morphological characters of 40 Populus taxa to reconstruct highly supported relationships of genus Populus. Relationships among the 60 taxa of Salicaceae strongly supported two monophyletic genera: Populus and Salix. Chosenia was nested within the genus Salix , and five clades within Populus were divided. Clade I included the three taxa P. euphratica, P. pruinosa , and P. ilicifolia. Clade II contained thirteen taxa [ P. adenopoda, P. alba, P. bolleana, P. davidiana, P. hopeiensis, P. nigra, P. qiongdaoensis, P. rotundifolia, P. rotundifolia var. duclouxiana, P. tremula, P. tremula × alba, P. tomentosa , and P. tomentosa (NC)]. Clade III included the ten taxa P. haoana, P. kangdingensis, P. lasiocarpa, P. pseudoglauca, P. qamdoensis, P. schneideri, P. simonii, P. szechuanica, P. szechuanica var. tibetica , and P. yunnanensis. Clade IV included P. cathayana, P. gonggaensis, P. koreana, P. laurifolia, P. trinervis, P. wilsonii , and P. xiangchengensis. The last clade comprised P. angustifolia, P. balsamifera, P. deltoides, P. deltoides × nigra, P. fremontii, P. mexicana , and P. trichocarpa. This phylogeny is also supported by morphological traits, including bark smoothness, bud size, petiole shape, leaf inflorescence, male anther length and male anther tip. [ABSTRACT FROM AUTHOR]

Methods for constructing trees using DNA sequences, known as molecular phylogenetics, have been applied to analyses of phylogenetic origin, evolutionary relatedness and taxonomic classification. Combining data sequenced in this study and downloaded from GenBank, we sampled 112 (chloroplast data) / 122 (ITS data) specimens belonging to 49 (chloroplast data) / 46 (ITS data) poplar species or hybrids from six (chloroplast data) / five sections (ITS data). Maximum parsimony and Bayesian inference were used to analyze phylogenetic relationships within the genus Populus based on eight chloroplast combinations and ITS regions. The results suggested that Bayesian inference might be more suitable for the phylogenetic reconstruction of Populus. All Populus species could be divided into two clades: clade 1, including subclades 1 and 2, and clade 2, including subclades 3 and 4. Species within clade 1, involving five sections except for Leuce, clustered coinciding with their two specific main geographical distribution areas: China (subclade 1) and North America (subclade 2). Clustering in subclade 3, section Leuce was confirmed to be of monophyletic origin and independent evolution. Its two subsections, namely Albidae and Trepidae, could be separated by chloroplast data but had frequent gene flow based on ITS data. Phylogeny analysis based on chloroplast data demonstrated once more that section Aigeiros was paraphyletic and further showed that the P. deltoides lineage is restricted in subclade 2 and that P. nigra lineage, located in subclade 3, originated from a hybrid of which an Albidae ancestor species was the material parent. Similarly, section Tacamahaca was found to be paraphyletic and had two lineages: a clade 1 lineage, such as P. cathayana, and a clade 2 lineage, such as P. simonii. Section Leucoides was paraphyletic and closely linked to section Tacamahaca. Their section boundaries were not conclusively delimitated by sequencing information. [ABSTRACT FROM AUTHOR]

Background: Abnormal apoptosis of lung endothelial cells has been observed in emphysematous lung tissue and has been suggested to be an important upstream event in the pathogenesis of chronic obstructive pulmonary disease (COPD). Studies have shown that microRNAs (miRNAs) contribute to the pathogenesis of pulmonary diseases by regulating cell apoptosis. The present study was designed to investigate the expression of microRNA-34a (miR-34a) in human pulmonary microvascular endothelial cells (HPMECs) exposed to cigarette smoke extract (CSE), and the potential regulatory role of miR-34a in endothelial cell apoptosis.Results: Our results showed that the expression of miR-34a was significantly increased in CSE-treated HPMECs, and inhibiting miR-34a attenuated CSE-induced HPMEC apoptosis. Furthermore, expression of Notch-1, a receptor protein in the Notch signalling pathway, was decreased and was inversely correlated with miR-34a expression in HPMECs treated with CSE. Computational miRNA target prediction confirmed that Notch-1 is a target of miR-34a. Luciferase reporter assay further confirmed the direct interaction between miR-34a and the 3'-untranslated region (UTR) of Notch-1. Restoration of Notch-1 pathway was able to partially block the effect of miR-34a on HPMEC apoptosis. These results indicate that Notch-1 is a critical downstream target of miR-34a in regulating the CSE-induced HPMEC apoptosis.Conclusions: Our results suggest that miR-34a plays a key role in CSE-induced endothelial cell apoptosis by directly regulating its target gene Notch-1 in endothelial cells. [ABSTRACT FROM AUTHOR]

MDR1 is highly expressed in MDR A2780DX5 ovarian cancer cells, MDR SGC7901R gastric cancer cells and recurrent tumours. It pumps cytoplasmic agents out of cells, leading to decreased drug accumulation in cells and making cancer cells susceptible to multidrug resistance. Here, we identified that miR-495 was predicted to target ABCB1, which encodes protein MDR1. To reduce the drug efflux and reverse MDR in cancer cells, we overexpressed a miR-495 mimic in SGC7901R and A2780DX cells and in transplanted MDR ovarian tumours in vivo. The results indicated that the expression of MDR1 in the above cells or tumours was suppressed and that subsequently the drug accumulation in the MDR cells was decreased, cell death was increased, and tumour growth was inhibited after treatment with taxol-doxorubicin, demonstrating increased drug sensitivity. This study suggests that pre-treatment with miR-495 before chemotherapy could improve the curative effect on MDR1-based MDR cancer. [ABSTRACT FROM AUTHOR]

Poncirus polyandra, a plant species with extremely small populations endemic to Fumin county of Yunnan province, has been classified as a national second-class protected wild plant. In this study, we assembled its complete chloroplast genome. The total genome size of P. polyandra was 160,211 bp in length, containing a large single-copy region of 87,406 bp, a small single-copy region of 18,771 bp, and a pair of inverted repeat regions of 27,017 bp. The all GC content of P. polyandra chloroplast genome was 38.4%. It contains 137 function genes, including 92 protein-coding genes, 37 tRNA genes, and eight rRNA ribosomal genes, 14 genes contain a single intron, and three genes have two introns. Phylogenetic analysis results strongly supported that P. polyandra was closely related to the genera of Citrus. [ABSTRACT FROM AUTHOR]

Populus tomentosa narrow crown [P. tomentosa (NC)], natural distributes in northern China, is an economically important ecotype of P. tomentosa. In this study, we assembled its complete chloroplast (cp) genome. The total genome size of P. tomentosa (NC) is 156,368 bp in length, containing a large single copy region of 84,623 bp, a small single copy region of 16,533 bp, and a pair of inverted repeat regions of 27,606 bp. We annotated 130 genes in the genome, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, 12 genes of which have 1 intron and 3 genes contain 2 introns. The overall GC content of the whole genome is 36.8%. Phylogenetic analysis using 24 complete cp genome of Salicaceae suggested that P. tomentosa (NC) is most closely related to P. alba. var. pyramidalis. [ABSTRACT FROM AUTHOR]

The complete sequence of the circular mitochondrial (mt) DNA of Populus rotundifolia var. duclouxiana is presented in this study. The size of the P. rotundifolia var. duclouxiana mt genome was 775,549 bp and the GC content of the genome was 44.8%. The P. rotundifolia var. duclouxiana mt genome encoded 58 genes, including 33 protein-coding genes, 22 tRNA genes, and three rRNA genes. Among the 58 genes, three genes contained one intron, one gene contained three introns, and four genes contained four introns. Phylogenetic analysis using seven complete mt genomes of Salicaceae supported that P. rotundifolia var. duclouxiana is most closely related to P. davidiana. [ABSTRACT FROM AUTHOR]

This retrospective study aims to examine the association of plasma Epstein-Barr virus- (EBV-) DNA levels with the tumor volume and prognosis in patients with locally advanced nasopharyngeal carcinoma (NPC). A total of 165 patients with newly diagnosed locally advanced NPC were identified from September 2011 to July 2012. EBV-DNA was detected using fluorescence quantitative polymerase chain reaction (PCR) amplification. The tumor volume was calculated by the systematic summation method of computer software. The median copy number of plasma EBV-DNA before treatment was 3790 copies/mL. The median gross tumor volume of the primary nasopharyngeal tumor (GTVnx), the lymph node lesions (GTVnd), and the total GTV before treatment were 72.46, 23.26, and 106.25 cm3, respectively; the EBV-DNA levels were significantly correlated with the GTVnd and the total GTV (P<0.01). The 2-year overall survival (OS) rates in patients with positive and negative pretreatment plasma EBV-DNA were 100% and 98.4% (P=1.000), and the disease-free survival (DFS) rates were 94.4% and 80.8% (P=0.044), respectively. These results indicate that high pretreatment plasma EBV-DNA levels in patients with locally advanced NPC are associated with the degree of lymph node metastasis, tumor burden, and poor prognosis. [ABSTRACT FROM AUTHOR]

Background: The widespread use of clopidogrel alone or in combination with aspirin may result in gastrointestinal mucosal injury, clinically represented as recurrent ulceration and bleeding complications. Our recent work suggested that clopidogrel significantly induced human gastric epithelial cell (GES-1) apoptosis and disrupted gastric mucosal barrier, and that a p38 MAPK inhibitor could attenuate such injury. However, their exact mechanisms are largely unknown. Methods: The GES-1 cells were used as a model system, the effects of clopidogrel on the whole gene expression profile were evaluated by human gene expression microarray and gene ontology analysis, changes of the mRNA and protein expression were determined by real-time PCR and Western blot analysis, and cell viability and apoptosis were measured by MTT assay and flow cytometry analysis, respectively. Results: Gene microarray analysis identified 79 genes that were differentially expressed (P<0.05 and fold-change >3) when cells were treated with or without clopidogrel. Gene ontology analysis revealed that response to stress and cell apoptosis dysfunction were ranked in the top 10 cellular events being affected, and that the major components of endoplasmic reticulum stress-mediated apoptosis pathway – CHOP and TRIB3– were up-regulated in a concentration- and time-dependent manner when cells were treated with clopidogrel. Pathway analysis demonstrated that multiple MAPK kinases were phosphorylated in clopidogrel-treated GES-1 cells, but that only SB-203580 (a p38-specific MAPK inhibitor) attenuated cell apoptosis and CHOP over-expression, both of which were induced by clopidogrel. Conclusions: Increased endoplasmic reticulum stress response is involved in clopidogrel-induced gastric mucosal injury, acting through p38 MAPK activation. [ABSTRACT FROM AUTHOR]

ABSTRACT Motion planning is an important problem in character animation and interactive simulation. However, few planning methods have considered domain-specific knowledge that governs the agent's behaviors, and none of them is capable of planning the interactive task in which the agent interacts with the objects in the virtual environment. This paper presents a novel method to plan the interactive task based on Q-learning for intelligent characters. The approach can be described as a three-phase framework: data preprocessing phase, controller learning phase, and motion-synthesis phase. In the data preprocessing phase, we abstract the motion clips as high-level behaviors and construct the interactive behavior graph (IBG) to define the interactive capabilities of the agent in terms of interactive features. For the controller training phase, with IBG, Q-learning algorithm is employed to train the control policy in the discrete domain with interactive features. In the motion-synthesis phase, the optimal motion sequences can be generated by following the policy to accomplish the interactive task finally. The experimental results demonstrate that the uniform framework can generate reasonable and realistic motion sequences to plan interactive task in complex environment. Copyright © 2012 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

The Toxicodendron vernicifluum cv. Dahongpao is an elite natural triploid lacquer tree with high economic and medicinal value. Therefore, in this study, we first characterize T. vernicifluum cv. Dahongpao complete chloroplast (cp) genome sequence. The complete cp genome sequence of T. vernicifluum cv. Dahongpao, with 38.0% GC content, is 159,571 bp in length. The genome presents a typical quadripartite structure with two inverted repeat regions (each 26,511 bp in length), separated by one large single-copy region and one small single-copy region (87,475 and 19,074 bp in length, respectively). The overall GC content is 38%, while in the LSC, SSC, and IR regions the GC contents are 36.1%, 32.6%, and 43.0%, respectively. The cp genome encodes 131 functional genes, of which 114 genes are single-copy, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis using maximum likelihood (ML) strongly support that T. vernicifluum cv. Dahongpao has a close phylogenetic relationship with Rhus chinensis and Pistacia weinmaniifolia. [ABSTRACT FROM AUTHOR]

The complete chloroplast genome sequence of Populus xiangchengensis C. Wang et Tung, an endemic species in southwest China, is presented in this study. The total genome size is 156,465 bp, with a typical quadripartite structure including a pair of inverted repeat (IRs, 27,570 bp) regions separated by a large single copy (LSC, 84,812 bp) region and a small single copy (SSC, 16,513 bp) region. The overall GC content of P. xiangchengensis plastid genome is 36.74%. The genome contains 130 genes, including 85 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. Among these genes, 12 genes have one intron and three genes contain two introns. The phylogenetic tree based on 26 complete plastomes of Salicaceae support close relationships among P. xiangchengensis, P. cathayana, and P. szechuanica. [ABSTRACT FROM AUTHOR]

Inverted cuttings of Populus yunnanensis remain alive by rooting from the original morphological apex and sprouting from the base, but the lateral branches exhibit less vigorous growth than those of the upright plant. In this study, we examined the changes in hormone contents, oxidase activities, and transcriptome profiles between upright and inverted cuttings of P. yunnanensis. The results showed that the indole-3-acetic acid (IAA) and gibberellic acid (GA3) contents were significantly lower in inverted cuttings than in upright cuttings only in the late growth period (September and October), while the abscisic acid (ABA) level was always similar between the two direction types. The biosynthesis of these hormones was surprisingly unrelated to the inversion of P. yunnanensis during the vegetative growth stage (July and August). Increased levels of peroxidases (PODs) encoded by 13 differentially expressed genes (DEGs) served as lignification promoters that protected plants against oxidative stress. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that most DEGs (107) were related to carbohydrate metabolism. Furthermore, altered activities of uridine diphosphate (UDP)-sugar pyrophosphorylase (USP, 15 DEGs) for nucleotide sugars, pectin methylesterase (PME, 7 DEGs) for pectin, and POD (13 DEGs) for lignin were important factors in the response of the trees to inversion, and these enzymes are all involved cell wall metabolism. [ABSTRACT FROM AUTHOR]