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Cutaneous malignant melanoma is one of the most lethal cutaneous malignancies. Accumulating evidence has demonstrated the potential influence of long non-coding RNAs (lncRNAs) in biological behaviors of melanoma. Herein, we reported a novel lncRNA, lnc-PKNOX1-1 and systematically studied its functions and possible molecular mechanisms in melanoma. Reverse transcription-quantitative PCR assay showed that lnc-PKNOX1-1 was significantly decreased in melanoma cells and tissues. Low lnc-PKNOX1-1 expression was significantly correlated with invasive pathological type and Breslow thickness of melanoma. In vitro and in vivo experiments showed lnc-PKNOX1-1 dramatically inhibited melanoma cell proliferation, migration and invasion. Mechanically, protein microarray analysis suggested that interleukin-8 (IL-8) was negatively regulated by lnc-PKNOX1-1 in melanoma, which was confirmed by western blot and ELISA. Western blot analysis also showed that lnc-PKNOX1-1 could promote p65 phosphorylation at Ser536 in melanoma. Subsequent rescue assays proved IL-8 overexpression could partly reverse the tumor-suppressing function of lnc-PKNOX1-1 overexpression in melanoma cells, indicating that lnc-PKNOX1-1 suppressed the development of melanoma by regulating IL-8. Taken together, our study demonstrated the tumor-suppressing ability of lnc-PKNOX1-1 in melanoma, suggesting its potential as a novel diagnostic biomarker and therapeutic target for melanoma. [ABSTRACT FROM AUTHOR]

Plant non-specific lipid transfer proteins (nsLTPs) are small, cysteine-rich proteins that play significant roles in biotic and abiotic stress responses; however, the molecular mechanism of their functions against viral infections remains unclear. In this study, we employed virus-induced gene-silencing and transgenic overexpression to functionally analyse a type-I nsLTP in Nicotiana benthamiana , NbLTP1 , in the immunity response against tobacco mosaic virus (TMV). NbLTP1 was inducible by TMV infection, and its silencing increased TMV-induced oxidative damage and the production of reactive oxygen species (ROS), compromised local and systemic resistance to TMV, and inactivated the biosynthesis of salicylic acid (SA) and its downstream signaling pathway. The effects of NbLTP1 -silencing were partially restored by application of exogenous SA. Overexpressing NbLTP1 activated genes related to ROS scavenging to increase cell membrane stability and maintain redox homeostasis, confirming that an early ROS burst followed by ROS suppression at the later phases of pathogenesis is essential for resistance to TMV infection. The cell-wall localization of NbLTP1 was beneficial to viral resistance. Overall, our results showed that NbLTP1 positively regulates plant immunity against viral infection through up-regulating SA biosynthesis and its downstream signaling component, NONEXPRESSOR OF PATHOGENESIS-RELATED 1 (NPR1), which in turn activates pathogenesis-related genes, and by suppressing ROS accumulation at the later phases of viral pathogenesis. [ABSTRACT FROM AUTHOR]

Initiation and progression of leaf senescence are triggered by various environmental stressors and phytohormones. Jasmonic acid (JA) and darkness accelerate leaf senescence in plants. However, the mechanisms that integrate these two factors to initiate and regulate leaf senescence have not been identified. Here, we report a transcriptional regulatory module centred on a novel tomato WRKY transcription factor, SlWRKY37, responsible for both JA- and dark-induced leaf senescence. The expression of SlWRKY37 , together with SlMYC2 , encoding a master transcription factor in JA signalling, was significantly induced by both methyl jasmonate (MeJA) and dark treatments. SlMYC2 binds directly to the promoter of SlWRKY37 to activate its expression. Knock out of SlWRKY37 inhibited JA- and dark-induced leaf senescence. Transcriptome analysis and biochemical experiments revealed SlWRKY53 and SlSGR1 (S. lycopersicum senescence-inducible chloroplast stay-green protein 1) as direct transcriptional targets of SlWRKY37 to control leaf senescence. Moreover, SlWRKY37 interacted with a VQ motif-containing protein SlVQ7, and the interaction improved the stability of SlWRKY37 and the transcriptional activation of downstream target genes. Our results reveal the physiological and molecular functions of SlWRKY37 in leaf senescence, and offer a target gene to retard leaf yellowing by reducing sensitivity to external senescence signals, such as JA and darkness. [ABSTRACT FROM AUTHOR]

Phytomelatonin is a small multifunctional molecule found ubiquitously in plants, which plays an important role in plant growth, development, and biotic and abiotic stress responses. The classical biosynthetic and metabolic pathways of phytomelatonin have been elucidated, and uncovering alternative pathways has deepened our understanding of phytomelatonin synthesis. Phytomelatonin functions mainly via two pathways. In the direct pathway, phytomelatonin mediates the stress-induced reactive oxygen species burst through its strong antioxidant capacity. In the indirect pathway, phytomelatonin acts as a signal to activate signaling cascades and crosstalk with other plant hormones. The phytomelatonin receptor PMTR1/CAND2 was discovered in 2018, which enhanced our understanding of phytomelatonin function. This review summarizes the classical and potential pathways involved in phytomelatonin synthesis and metabolism. To elucidate the functions of phytomelatonin, we focus on the crosstalk between phytomelatonin and other phytohormones. We propose two models to explain how PMTR1 transmits the phytomelatonin signal through the G protein and MAPK cascade. This review will facilitate the identification of additional signaling molecules that function downstream of the phytomelatonin signaling pathway, thus improving our understanding of phytomelatonin signal transmission. [ABSTRACT FROM AUTHOR]

Objectives: To evaluate the correlation between tumor-infiltrating lymphocytes (TILs) and the viral load of high-risk human papillomavirus (HR-HPV) in cervical cancer patients.Methods: A total of 62 cervical cancer patients were recruited during 1993-1994 and assigned into four groups treated with radiotherapy alone or radiotherapy combined with chemotherapy and/or thermotherapy. Ki67+ tumor cells, CD4+, CD8+, FoxP3+, OX40+ and granzyme B+ TILs were detected by immunohistochemistry. The viral load of HR-HPV in biopsy tissues before therapy was detected by in situ hybridization.Results: The patients with high HPV viral load showed a significantly lower 15-year survival rate and an advanced International Federation of Gynecology and Obstetrics (FIGO) stage and increased recurrence rate. The distribution of Ki67+ tumor cells, FoxP3+ TILs, and CD8+/FoxP3+ ratio was obviously different between low and high HPV viral load groups. A worse clinical outcome was also implicated with increased HPV viral load tested by Cox regression analysis.Conclusions: Patients with increased HR-HPV viral load tend to be resistant to therapy with decreased immune surveillance in the immune microenvironment. Thus, HR-HPV viral load would influence the local immune microenvironment, and then further affect the survival of cervical cancer patients. [ABSTRACT FROM AUTHOR]

Experiments that longitudinally collect RNA sequencing (RNA‐seq) data can provide transformative insights in biology research by revealing the dynamic patterns of genes. Such experiments create a great demand for new analytic approaches to identify differentially expressed (DE) genes based on large‐scale time‐course count data. Existing methods, however, are suboptimal with respect to power and may lack theoretical justification. Furthermore, most existing tests are designed to distinguish among conditions based on overall differential patterns across time, though in practice, a variety of composite hypotheses are of more scientific interest. Finally, some current methods may fail to control the false discovery rate. In this paper, we propose a new model and testing procedure to address the above issues simultaneously. Specifically, conditional on a latent Gaussian mixture with evolving means, we model the data by negative binomial distributions. Motivated by Storey (2007) and Hwang and Liu (2010), we introduce a general testing framework based on the proposed model and show that the proposed test enjoys the optimality property of maximum average power. The test allows not only identification of traditional DE genes but also testing of a variety of composite hypotheses of biological interest. We establish the identifiability of the proposed model, implement the proposed method via efficient algorithms, and demonstrate its good performance via simulation studies. The procedure reveals interesting biological insights, when applied to data from an experiment that examines the effect of varying light environments on the fundamental physiology of the marine diatom Phaeodactylum tricornutum. [ABSTRACT FROM AUTHOR]

This study was conducted to investigate the effects of Clostridium butyricum addition to diets in late gestation and lactation on the reproductive performance and gut microbiota for sows. A total of 180 healthy Landrace × Yorkshire sows at 90 d of gestation were randomly assigned to one of four groups, with 45 replicates per group, receiving a basal commercial diet (Control, 0% C. butyricum) or diet added with 0.1% C. butyricum (1 × 108 CFU/kg of feed), 0.2% C. butyricum (2 × 108 CFU/kg of feed), 0.4% C. butyricum (4 × 108 CFU/kg of feed), respectively. The experiment was conducted from 90 d of gestation to weaning at 21 d of lactation. The results showed that the interval between piglet born was linearly (P < 0.05) decreased, and the duration of farrowing was significantly (quadratic, P < 0.05) shortened as C. butyricum addition increased. There was a linear (P < 0.05) increase in litter weight at weaning and litter weight gain. The concentrations of IgG and IgM in colostrum, and IgM in milk were linearly increased (P < 0.05) as C. butyricum addition. Serum MDA concentrations of sows at parturition and 14 d in lactation, and piglets at 14 and 21 d of age were linearly (P < 0.05) decreased, respectively. The serum total antioxidant capacity concentrations of sows at parturition and 14 and 21 d in lactation, and piglets at 14 and 21 d of age were linearly (P < 0.05) increased as C. butyricum addition, respectively. There was a linear decrease in the serum endotoxin concentration of sows on 21 d in lactation (P < 0.05). The serum cortisol concentrations of piglets at 14 and 21 d of age were both significantly (quadratic, P < 0.05) decreased. The 0.2% C. butyricum increased the relative abundance of Bacteroidetes (P = 0.016) at phylum level, Prevotellaceae_NK3B31_group , Prevotella_1 , Prevotellaceae_UCG-003 , Prevotella_9 , Alloprevotella (P < 0.05) at genus level, and decreased the relative abundance of Proteobacteria , Gemmatimonadetes , Actinobacteria (P < 0.001) at phylum level, and Clostridium_sensu_stricto_1 , Streptococcus , Escheruchia-Shigella , Sphingomonas , Succinivibrio (P < 0.05) at genus level and Firmicutes/Bacteroidetes ratio (P = 0.020). In conclusion, the present research indicated that dietary addition with C. butyricum could shorten the duration of farrowing and enhance the growth performance of suckling piglets. Moreover, 0.2% C. butyricum administration to sows changed the composition of intestinal microbiota, especially increased the relative abundance of Prevotella. [ABSTRACT FROM AUTHOR]

This study was conducted to investigate the effects of Clostridium butyricum addition to diets in late gestation and lactation on the reproductive performance and gut microbiota for sows. A total of 180 healthy Landrace × Yorkshire sows at 90 d of gestation were randomly assigned to one of four groups, with 45 replicates per group, receiving a basal commercial diet (Control, 0% C. butyricum) or diet added with 0.1% C. butyricum (1 × 108 CFU/kg of feed), 0.2% C. butyricum (2 × 108 CFU/kg of feed), 0.4% C. butyricum (4 × 108 CFU/kg of feed), respectively. The experiment was conducted from 90 d of gestation to weaning at 21 d of lactation. The results showed that the interval between piglet born was linearly (P < 0.05) decreased, and the duration of farrowing was significantly (quadratic, P < 0.05) shortened as C. butyricum addition increased. There was a linear (P < 0.05) increase in litter weight at weaning and litter weight gain. The concentrations of IgG and IgM in colostrum, and IgM in milk were linearly increased (P < 0.05) as C. butyricum addition. Serum MDA concentrations of sows at parturition and 14 d in lactation, and piglets at 14 and 21 d of age were linearly (P < 0.05) decreased, respectively. The serum total antioxidant capacity concentrations of sows at parturition and 14 and 21 d in lactation, and piglets at 14 and 21 d of age were linearly (P < 0.05) increased as C. butyricum addition, respectively. There was a linear decrease in the serum endotoxin concentration of sows on 21 d in lactation (P < 0.05). The serum cortisol concentrations of piglets at 14 and 21 d of age were both significantly (quadratic, P < 0.05) decreased. The 0.2% C. butyricum increased the relative abundance of Bacteroidetes (P = 0.016) at phylum level, Prevotellaceae_NK3B31_group , Prevotella_1 , Prevotellaceae_UCG-003 , Prevotella_9 , Alloprevotella (P < 0.05) at genus level, and decreased the relative abundance of Proteobacteria , Gemmatimonadetes , Actinobacteria (P < 0.001) at phylum level, and Clostridium_sensu_stricto_1 , Streptococcus , Escheruchia-Shigella , Sphingomonas , Succinivibrio (P < 0.05) at genus level and Firmicutes/Bacteroidetes ratio (P = 0.020). In conclusion, the present research indicated that dietary addition with C. butyricum could shorten the duration of farrowing and enhance the growth performance of suckling piglets. Moreover, 0.2% C. butyricum administration to sows changed the composition of intestinal microbiota, especially increased the relative abundance of Prevotella. [ABSTRACT FROM AUTHOR]

Given detailed microscale simulations of complicated physical processes, the multiscale gap-tooth scheme empowers efficient macroscale simulations. By coupling small patches of simulations over unsimulated physical gaps, large savings in computational time are possible. So far the gap-tooth scheme has been developed for dissipative systems, but wave-like systems arise in many applications. This article develops the gap-tooth scheme for the case of non-linear microscale simulations of wave-like systems. We show that classic macroscale interpolation provides a generic coupling between patches that achieves arbitrarily high-order consistency between the multiscale scheme and the underlying microscale dynamics. Eigen-analysis indicates that the resultant gap-tooth scheme empowers feasible computation of large-scale simulations of wave-like dynamics with complicated underlying physics. For example, we implement numerical simulations of dam-breaking waves by the gap-tooth scheme. Comparison between a gap-tooth simulation, a microscale simulation over the whole domain, and some published experimental data on dam-breaking demonstrates that the gap-tooth scheme feasibly computes large-scale, highly non-linear, wave-like dynamics with major computational savings. [ABSTRACT FROM AUTHOR]

In this study, based on a comprehensive numerical simulation of self-consistent charging, we investigate the formation, evolution and influencing factors of space charge distributions for a grounded insulating thin film of SiO2 negatively charged by a keV non-penetrating focused electron beam. The simulated space charge presents first positive distributions and then negative ones along both the radial and depth directions because of the difference between electron and hole transports. The variations in distribution occur within a range of the minimum potential acting as a potential barrier for carrier transport. The negative space charge is distributed more widely and deeply, though its peak value in density is usually lower than that of the positive one. Electrons trapped outside the minimum potential range dominate the strength of negative charging. With the increase in potential barrier and the occurrence of leakage current, the space charge eventually reaches equilibrium and exhibits an approximately one-dimensional axial distribution outside the minimum potential range. Distribution features of the space charge density in the equilibrium state correlate with the film and beam parameters via transients of the leakage current. These results and analyses provide new insights into the negative charging effects involved in various electron-beam-based surface microscopic methods, analyses and fabrication techniques. [ABSTRACT FROM PUBLISHER]

Image blurring of MeV transmission electrons for gold nanoparticles on the top surface of micrometer-thick specimens has been investigated using the Monte Carlo simulation. Both the simulated line density profile and therefore image blurring were in good agreement with the experimental ones in the ultrahigh voltage electron microscope. Quantitative effects of specimen thickness and electron energy on image blurring were presented, in which the specimen thickness had a greater influence. Image blurring was demonstrated to be caused mainly by multiple elastic scattering, but it could be reduced to several nanometers for a 5 µm thick epoxy-resin specimen at the electron energy of 2 MeV. [ABSTRACT FROM PUBLISHER]

We presented an automatic method for detecting and tracking colloidal gold fiducial markers for alignment in electron tomography (ET). The second-order derivative of direction was used to detect a fiducial marker accurately. The detection was optimized to be selective to the size of fiducial markers. A preliminary tracking result from the normalized correlation coefficient was refined using the detector. A constraint model considering the relationship among the fiducial markers on different images was developed for removing outlier. The three-dimensional positions of the detected fiducial markers and the projection parameters of tilt images were calculated for post process. The accuracy of detection and tracking results was evaluated from the residues by the software IMOD. Application on transmission electron microscopic images also indicated that the presented method could provide a useful approach to automatic alignment in ET. [ABSTRACT FROM AUTHOR]

The ultra-high voltage electron microscope (UHVEM) H-3000 with the world highest acceleration voltage of 3 MV can observe remarkable three dimensional microstructures of microns-thick samples[1]. Acquiring a tilt series of electron tomography is laborious work and thus an automatic technique is highly desired. We proposed the Auto-Focus system using image Sharpness (AFS)[2,3] for UHVEM tomography tilt series acquisition. In the method, five images with different defocus values are firstly acquired and the image sharpness are calculated. The sharpness are then fitted to a quasi-Gaussian function to decide the best focus value[3]. Defocused images acquired by the slow scan CCD (SS-CCD) camera (Hitachi F486BK) are of high quality but one minute is taken for acquisition of five defocused images.In this study, we introduce a high-definition video camera (HD video camera; Hamamatsu Photonics K. K. C9721S) for fast acquisition of images[4]. It is an analog camera but the camera image is captured by a PC and the effective image resolution is 1280×1023 pixels. This resolution is lower than that of the SS-CCD camera of 4096×4096 pixels. However, the HD video camera captures one image for only 1/30 second. In exchange for the faster acquisition the S/N of images are low. To improve the S/N, 22 captured frames are integrated so that each image sharpness is enough to become lower fitting error. As countermeasure against low resolution, we selected a large defocus step, which is typically five times of the manual defocus step, to discriminate different defocused images.By using HD video camera for autofocus process, the time consumption for each autofocus procedure was reduced to about six seconds. It took one second for correction of an image position and the total correction time was seven seconds, which was shorter by one order than that using SS-CCD camera. When we used SS-CCD camera for final image capture, it took 30 seconds to record one tilt image. We can obtain a tilt series of 61 images within 30 minutes. Accuracy and repeatability were good enough to practical use (Figure 1). We successfully reduced the total acquisition time of a tomography tilt series in half than before.Fig. 1.Objective lens current change with a tilt angle during acquisition of tomography series (Sample: a rat hepatocyte, thickness: 2 m, magnification: 4k, acc. voltage: 2 MV). Tilt angle range is ±60 degree with 2 degree step angle. Two series were acquired in the same area. Both data were almost same and the deviation was smaller than the minimum step by manual, so auto-focus worked well.We also developed a computer-aided three dimensional (3D) visualization and analysis software for electron tomography "HawkC" which can sectionalize the 3D data semi-automatically[5,6]. If this auto-acquisition system is used with IMOD reconstruction software[7] and HawkC software, we will be able to do on-line UHVEM tomography. The system would help pathology examination in the future.This work was supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, under a Grant-in-Aid for Scientific Research (Grant No. 23560024, 23560786), and SENTAN, Japan Science and Technology Agency, Japan. [ABSTRACT FROM PUBLISHER]