Probing Single DNA Molecule Transport Using Fabricated Nanopores

Nanopores can serve as high throughput, single-molecule sensing devices that provide insight into the distribution of static and dynamic molecular activities, properties, or interactions. We have studied double stranded DNA electrophoretic transport dynamics through fabricated nanopores in silicon nitride. A fabricated pore enables us to interrogate a broader range of molecules with a wider range of conditions than can be investigated in a self-assembled protein pore in a lipid membrane.Molecular and Cellular Biolog

Data from: How much do phenotypic plasticity and local genetic variation contribute to phenotypic divergences along environmental gradients in widespread invasive plants? A meta-analysis

For introduced species that have spread across a wide distributional range, phenotypic plasticity (PLA) has often been proposed as an important contributor to invasion success, because it increases the survival rate during initial colonization. In contrast, local genetic variation (LOC) has also been proposed to be important, because it could allow invaders to evolve high performance in a new habitat. While evolutionary ecologists have long been interested in understanding genetic mechanisms that allow rapid colonization and spread of species, until recently experimental tests of these concepts have been limited. As a step towards generalization in our understanding of the importance of PLA and LOC, we review the current state of the literature on this topic using meta-analysis. Here, we focused on three fundamental questions: 1) which strategy, PLA or LOC, better explains the phenotypic divergences during invader range expansion across different environmental gradients? 2) Which species characteristics correlate with the occurrence of these different phenomena? And 3) does the detection of PLA versus LOC depend on the trait studied? Using meta-analysis we found that plasticity explained a higher proportion of phenotypic variation regardless of the environmental gradients studied or plant growth forms. PLA predominated in clonal, self-compatible and perennial species, while LOC predominated in annual species. The patterns were trait-dependent: LOC was significantly more important than PLA in phenology, while opposite patterns were found in fecundity and biomass allocation. The frequent simultaneous detection of PLA and genotypic variation in PLA among invasive populations suggested that PLA might benefit from LOC to some extent. Our results also indicate that the contribution of plasticity to the competitive advantages of invasive plants may be more informative than the level of plasticity itself

Data file

All the F-, SS- and R-statistics for the calculation for the effect size for this meta analysis. Please refer to the equations for calculating the effect sizes in OIKOS02372 and the corresponding supporting information

Endoplasmic Reticulum Stress in Spinal Cord Contributes to the Development of Morphine Tolerance

Morphine tolerance remains an intractable problem, which hinders its prolonged use in clinical practice. Endoplasmic reticulum (ER) stress has been proved to play a fundamental role in the pathogenesis of Alzheimer’s disease, diabetes, atherosclerosis, cancer, etc. In this study, we provide the first direct evidence that ER stress may be a significant driver of morphine tolerance. Binding immunoglobulin protein (BiP), the ER stress marker, was significantly upregulated in neurons in spinal dorsal horn in rats being treated with morphine for 7 days. Additionally, chronic morphine treatment resulted in the activation of three arms of unfolded protein response (UPR): inositol-requiring enzyme 1/X-box binding protein 1 (IRE1/XBP1), protein kinase RNA-like ER kinase/eukaryotic initiation factor 2 subunit alpha (PERK/eIF2α), and activating transcription factor 6 (ATF6). More importantly, inhibiting either one of the three cascades could attenuate the development of morphine tolerance. Taken together, our results suggest that ER stress in spinal cord might contribute to the development of morphine tolerance. These findings implicate a potential clinical strategy for preventing morphine tolerance and may contribute to expanding the morphine usage in clinic

‘Triple clear’: a systematic and comprehensive surgical process for Campanacci grades II and III giant cell tumors of the bone, with or without pathological fracture and slight joint invasion

Abstract Background In recent years, researchers have proposed a number of adjuvant methods for extended curettage of giant cell tumors of the bone. However, various schemes have significant differences in efficacy and safety. Therefore, this article will describe an empirical expanded curettage protocol, ‘triple clear’, in detail to show the effect of the efficient surgical protocol. Method Patients with Campanacci grades II and III primary GCTB who were treated with either SR (n = 39) or TC (n = 41) were included. Various perioperative clinical indicators, including the therapy modality, operation time, Campanacci grade, and filling material were recorded and compared. The pain level was determined by the visual analog scale. Limb function was determined by the Musculoskeletal Tumour Society (MSTS) score. Follow-up time, recurrence rates, reoperation rates, and complication rates were also recorded and compared. Result The operation time was 135.7 ± 38.4 min in the TC group and 174.2 ± 43.0 min in the SR group (P < 0.05). The recurrence rates were 7.3% in the TC group and 8.3% in the SR group (P = 0.37). The MSTS scores at three months after surgery were 19.8 ± 1.5 in the TC group and 18.8 ± 1.3 in the SR group. The MSTS scores at two years were 26.2 ± 1.2 in the TC group and 24.3 ± 1.4 in the SR group (P < 0.05). Conclusion TC is recommended for patients with Campanacci grade II–III GCTB and for those with a pathological fracture or slight joint invasion. Bone grafts may be more suitable than bone cement in the long term

1,3-Pentadiene-Assistant Living Anionic Terpolymerization: Composition Impact on Kinetics and Microstructure Sequence Primary Analysis

The combination of a living anionic technology and a unique alternating strategy provided an exciting opportunity to prepare novel and well-defined poly(1,3-pentadiene-co-syrene-co-1,1-diphenylethylene) resins consisting of three alternating sequences of modules (A/B/C zwitterions). “A” being Styrene (St)/1,3-pentadiene (PD), “B” being diphenylethylene (DPE)/PD, “A” being DPE/St, respectively, A wide composition range of new polyolefin resins, i.e., poly (A-co-B), poly (A-co-C), and poly (B-co-C), with controlled molecular weight and very narrow molecular weight and composition distributions have been prepared by a one-pot living characteristic method. In the section of kinetic analysis, the terpolymer yields and kinetic parameters were strongly dependent on the feed/comonomer ratio as well as the content of the alternating structure. The competition copolymerization behaviors of A/B, B/C, and A/C were studied in detail in this work. By contrast, the microstructure and the thermal property of the resulting terpolymer were investigated via Nuclear magnetic resonance (NMR) and Differential scanning calorimetry (DSC) analysis. The results of 1H NMR tracking the change of [Aromatic ring]/[C=C] value indicated the distinctive copolymer-ization behavior of the selective “alternating-modules”. The glass transition temperature (Tg) was very sensitive to the terpolymer composition. By contrast to poly(A-ran-B) with only one obvious Tg, there were two Tgs in the A/C and B/C copolymerization cases. Moreover, the desirable high Tg ~ 140 °C resin was limited to the terpolymers with up to 50 mol % DPE. Finally, the “ABC-X” mechanism was proposed to interpret the unique terpolymerization behavior, which belongs to the classical “bond-forming initiation” theory

Efficient live and on-demand tiled HEVC 360 VR video streaming

360∘ panorama video displayed through Virtual Reality (VR) glasses or large screens offers immersive user experiences, but as such technology becomes commonplace, the need for efficient streaming methods of such high-bitrate videos arises. In this respect, the attention that 360∘ panorama video has received lately is huge. Many methods have already been proposed, and in this paper, we shed more light on the different trade-offs in order to save bandwidth while preserving the video quality in the user’s field-of-view (FoV). Using 360∘ VR content delivered to a Gear VR head-mounted display with a Samsung Galaxy S7 and to a Huawei Q22 set-top-box, we have tested various tiling schemes analyzing the tile layout, the tiling and encoding overheads, mechanisms for faster quality switching beyond the DASH segment boundaries and quality selection configurations. In this paper, we present an efficient end-to-end design and real-world implementation of such a 360∘ streaming system. Furthermore, in addition to researching an on-demand system, we also go beyond the existing on-demand solutions and present a live streaming system which strikes a trade-off between bandwidth usage and the video quality in the user’s FoV. We have created an architecture that combines RTP and DASH, and our system multiplexes a single HEVC hardware decoder to provide faster quality switching than at the traditional GOP boundaries. We demonstrate the performance and illustrate the trade-offs through real-world experiments where we can report comparable bandwidth savings to existing on-demand approaches, but with faster quality switches when the FoV changes

Efficient live and on-demand tiled HEVC 360 VR video streaming

360∘ panorama video displayed through Virtual Reality (VR) glasses or large screens offers immersive user experiences, but as such technology becomes commonplace, the need for efficient streaming methods of such high-bitrate videos arises. In this respect, the attention that 360∘ panorama video has received lately is huge. Many methods have already been proposed, and in this paper, we shed more light on the different trade-offs in order to save bandwidth while preserving the video quality in the user’s field-of-view (FoV). Using 360∘ VR content delivered to a Gear VR head-mounted display with a Samsung Galaxy S7 and to a Huawei Q22 set-top-box, we have tested various tiling schemes analyzing the tile layout, the tiling and encoding overheads, mechanisms for faster quality switching beyond the DASH segment boundaries and quality selection configurations. In this paper, we present an efficient end-to-end design and real-world implementation of such a 360∘ streaming system. Furthermore, in addition to researching an on-demand system, we also go beyond the existing on-demand solutions and present a live streaming system which strikes a trade-off between bandwidth usage and the video quality in the user’s FoV. We have created an architecture that combines RTP and DASH, and our system multiplexes a single HEVC hardware decoder to provide faster quality switching than at the traditional GOP boundaries. We demonstrate the performance and illustrate the trade-offs through real-world experiments where we can report comparable bandwidth savings to existing on-demand approaches, but with faster quality switches when the FoV changes

Structural insights into Xanthomonas campestris pv. campestris NAD+ biosynthesis via the NAM salvage pathway

Abstract Nicotinamide phosphoribosyltransferase (NAMPT) plays an important role in the biosynthesis of nicotinamide adenine dinucleotide (NAD+) via the nicotinamide (NAM) salvage pathway. While the structural biochemistry of eukaryote NAMPT has been well studied, the catalysis mechanism of prokaryote NAMPT at the molecular level remains largely unclear. Here, we demonstrated the NAMPT-mediated salvage pathway is functional in the Gram-negative phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc) for the synthesis of NAD+, and the enzyme activity of NAMPT in this bacterium is significantly higher than that of human NAMPT in vitro. Our structural analyses of Xcc NAMPT, both in isolation and in complex with either the substrate NAM or the product nicotinamide mononucleotide (NMN), uncovered significant details of substrate recognition. Specifically, we revealed the presence of a NAM binding tunnel that connects the active site, and this tunnel is essential for both catalysis and inhibitor binding. We further demonstrated that NAM binding in the tunnel has a positive cooperative effect with NAM binding in the catalytic site. Additionally, we discovered that phosphorylation of the His residue at position 229 enhances the substrate binding affinity of Xcc NAMPT and is important for its catalytic activity. This work reveals the importance of NAMPT in bacterial NAD+ synthesis and provides insights into the substrate recognition and the catalytic mechanism of bacterial type II phosphoribosyltransferases