Efficient QTL detection of flowering date in a soybean RIL population using the novel restricted two-stage multi-locus GWAS procedure.

KEY MESSAGE: Eighty-six R1 QTLs accounting for 89.92% phenotypic variance in a soybean RIL population were identified using RTM-GWAS with SNPLDB marker which performed superior over CIM and MLM-GWAS with BIN/SNPLDB marker. A population (NJRIKY) composed of 427 recombinant inbred lines (RILs) derived from Kefeng-1 × NN1138-2 (MGII × MGV, MG maturity group) was applied for detecting flowering date (R1) quantitative trait locus (QTL) system in soybean. From a low-depth re-sequencing (~ 0.75 ×), 576,874 SNPs were detected and organized into 4737 BINs (recombination breakpoint determinations) and 3683 SNP linkage disequilibrium blocks (SNPLDBs), respectively. Using the association mapping procedures "Restricted Two-stage Multi-locus Genome-wide Association Study" (RTM-GWAS), "Mixed Linear Model Genome-wide Association Study" (MLM-GWAS) and the linkage mapping procedure "Composite Interval Mapping" (CIM), 67, 36 and 10 BIN-QTLs and 86, 14 and 23 SNPLDB-QTLs were detected with their phenotypic variance explained (PVE) 88.70-89.92% (within heritability 98.2%), 146.41-353.62% (overflowing) and 88.29-172.34% (overflowing), respectively. The RTM-GWAS with SNPLDBs which showed to be more efficient and reasonable than the others was used to identify the R1 QTL system in NJRIKY. The detected 86 SNPLDB-QTLs with their PVE from 0.02 to 30.66% in a total of 89.92% covered 51 out of 104 R1 QTLs in 18 crosses in SoyBase and 26 out of 139 QTLs in a nested association mapping population, while the rest 29 QTLs were novel ones. From the QTL system, 52 candidate genes were annotated, including the verified gene E1, E2, E9 and J, and grouped into 3 categories of biological processes, among which 24 genes were enriched into three protein-protein interaction networks, suggesting gene networks working together. Since NJRIKY involves only MGII and MGV, the QTL/gene system among MG000-MGX should be explored further.

Folic acid-conjugated silica capped gold nanoclusters for targeted fluorescence/X-ray computed tomography imaging.

BACKGROUND: Gastric cancer is 2th most common cancer in China, and is still the second most common cause of cancer-related death in the world. Successful development of safe and effective nanoprobes for in vivo gastric cancer targeting imaging is a big challenge. This study is aimed to develop folic acid (FA)-conjugated silica coated gold nanoclusters (AuNCs) for targeted dual-modal fluorescent and X-ray computed tomography imaging (CT) of in vivo gastric cancer cells. METHOD: AuNCs were prepared, silica was coated on the surface of AuNCs, then folic acid was covalently anchored on the surface of AuNCs, resultant FA-conjugated AuNCs@SiO2 nanoprobes were investigated their cytotoxicity by MTT method, and their targeted ability to FR(+) MGC803 cells and FR(-) GES-1 cells. Nude mice model loaded with MGC803 cells were prepared, prepared nanoprobes were injected into nude mice via tail vein, and then were imaged by fluorescent and X-ray computed tomography (CT) imaging. RESULTS: FA-conjugated AuNCs@SiO2 nanoprobes exhibited good biocompatibility, and could target actively the FR(+) MGC-803 cells and in vivo gastric cancer tissues with 5 mm in diameter in nude mice models, exhibited excellent red emitting fluorescence imaging and CT imaging. CONCLUSION: The high-performance FA-conjugated AuNCs@SiO2 nanoprobes can target in vivo gastric cancer cells, can be used for fluorescent and CT dual-mode imaging, and may own great potential in applications such as targeted dual-mode imaging of in vivo early gastric cancer and other tumors with FR positive expression in near future.

High Frame Rate Video Reconstruction Based on an Event Camera.

Event-based cameras measure intensity changes (called 'events') with microsecond accuracy under high-speed motion and challenging lighting conditions. With the 'active pixel sensor' (APS), the 'Dynamic and Active-pixel Vision Sensor' (DAVIS) allows the simultaneous output of intensity frames and events. However, the output images are captured at a relatively low frame rate and often suffer from motion blur. A blurred image can be regarded as the integral of a sequence of latent images, while events indicate changes between the latent images. Thus, we are able to model the blur-generation process by associating event data to a latent sharp image. Based on the abundant event data alongside a low frame rate, easily blurred images, we propose a simple yet effective approach to reconstruct high-quality and high frame rate sharp videos. Starting with a single blurred frame and its event data from DAVIS, we propose the Event-based Double Integral (EDI) model and solve it by adding regularization terms. Then, we extend it to multiple Event-based Double Integral (mEDI) model to get more smooth results based on multiple images and their events. Furthermore, we provide a new and more efficient solver to minimize the proposed energy model. By optimizing the energy function, we achieve significant improvements in removing blur and the reconstruction of a high temporal resolution video. The video generation is based on solving a simple non-convex optimization problem in a single scalar variable. Experimental results on both synthetic and real datasets demonstrate the superiority of our mEDI model and optimization method compared to the state-of-the-art.

A single quantum dot-based fluorescence resonance energy transfer biosensor for antibody-free detection of ten-eleven translocation 1.

We developed a single quantum dot-based fluorescence resonance energy transfer biosensor for antibody-free detection of ten-eleven translocation 1 (TET1). This biosensor can sensitively detect TET1 in a homogeneous manner without the involvement of any specific antibodies, and it can be used for accurate measurement of TET1 activity in human neuroblastoma cells and the screening of TET1 inhibitors.

Deacetylation-activated construction of single quantum dot-based nanosensor for sirtuin 1 assay.

Sirtuin 1 (SIRT1) is an important histone deacetylase that regulates biological functions ranging from DNA repair to metabolism. The alteration of SIRT1 is associated with a variety of diseases including diabetes, inflammation, aging-related diseases, and cancers. Consequently, the detection of SIRT1 activity is of great therapeutic importance. Herein, we demonstrate for the first time the deacetylation-activated construction of single quantum dot (QD)-based nanosensor for sensitive SIRT1 assay. This nanosensor is composed of a Cy5-labeled peptide substrate and a streptavidin-coated QD. The peptide with one lysine acetyl group acts as both the Cy5 fluorophore carrier and the substrate for sensing SIRT1. In the presence of SIRT1, it removes the acetyl group in the acetylated peptide, and the resultant deacetylated peptide can react with the NHS-activated biotin reagent (sulfo-NHS-biotin) to form the biotinylated peptide. The multiple biotinylated peptides can assemble on single QD surface via biotin-streptavidin interaction, inducing efficient fluorescence resonance energy transfer (FRET) from the QD to Cy5, generating distinct Cy5 signal which can be simply quantified by total internal reflection fluorescence-based single-molecule detection. This single QD-based nanosensor can sensitively detect SIRT1 with a detection limit of as low as 3.91 pM, and it can be applied for the measurement of enzyme kinetic parameters and the screening of SIRT1 inhibitors. Moreover, this nanosensor can be used to detect the SIRT1 activity in cancer cells, providing a powerful platform for epigenetic research and SIRT1-targeted drug discovery.

Joint Stereo Video Deblurring, Scene Flow Estimation and Moving Object Segmentation.

Stereo videos for the dynamic scenes often show unpleasant blurred effects due to the camera motion and the multiple moving objects with large depth variations. Given consecutive blurred stereo video frames, we aim to recover the latent clean images, estimate the 3D scene flow and segment the multiple moving objects. These three tasks have been previously addressed separately, which fail to exploit the internal connections among these tasks and cannot achieve optimality. In this paper, we propose to jointly solve these three tasks in a unified framework by exploiting their intrinsic connections. To this end, we represent the dynamic scenes with the piece-wise planar model, which exploits the local structure of the scene and expresses various dynamic scenes. Under our model, these three tasks are naturally connected and expressed as the parameter estimation of 3D scene structure and camera motion (structure and motion for the dynamic scenes). By exploiting the blur model constraint, the moving objects and the 3D scene structure, we reach an energy minimization formulation for joint deblurring, scene flow and segmentation. We evaluate our approach extensively on both synthetic datasets and publicly available real datasets with fast-moving objects, camera motion, uncontrolled lighting conditions and shadows. Experimental results demonstrate that our method can achieve significant improvement in stereo video deblurring, scene flow estimation and moving object segmentation, over state-of-the-art methods.

Phase and size controllable synthesis of NaYbF4 nanocrystals in oleic acid/ionic liquid two-phase system for targeted fluorescent imaging of gastric cancer.

Upconversion nanocrystals with small size and strong fluorescent signals own great potential in applications such as biomolecule-labeling, in vivo tracking and molecular imaging. Herein we reported that NaYbF4: 25%Gd, 2%Tm upconversion nanocrystals with small size and strong fluorescent signals were controllably synthesized by oleic acid (OA)/ ionic liquid (IL) two-phase system for targeted fluorescent imaging of gastric cancer in vivo. The optimal synthesis condition of NaYbF4: 25%Gd, 2%Tm upconversion nanocrystals by OA/IL two-phase system was established, adding more metal ion such as Na(+) ion could facilitate the size control and crystal-phase transition, more importantly, markedly enhancing fluorescent intensity of beta-phase nanocrystals compared with traditional methods. Alpha-phase NaYbF4, 2%Tm upconversion nanocrystals with less than 10nm in diameter and beta-phase NaYbF4: 25%Gd, 2%Tm upconversion nanocrystals with 30 nm or so in diameter and strong fluorescent signals were obtained, these synthesized nanocrystals exhibited very low cytotoxicity. Folic acid-conjugated silica-modified beta-phase NaYbF4: 25%Gd, 2%Tm upconversion nanocrystals were prepared, could actively target gastric cancer tissues implanted into nude mice in vivo, and realized targeted fluorescent imaging. Folic acid-conjugated silica-modified NaYbF4: 25%Gd, 2%Tm upconversion nanocrystals show great potential in applications such as targeted near infared radiation fluorescent imaging, magnetic resonance imaging and targeted therapy of gastric cancer in the near future.

Folic acid-conjugated LaF3:Yb,Tm@SiO2 nanoprobes for targeting dual-modality imaging of upconversion luminescence and X-ray computed tomography.

Development of multimodal contrast agents for in vivo simultaneous multimodality imaging is an emerging interdiscipline that is paving the avenue toward the goal of personalized medicine. Herein, folic acid-conjugated silica-modified LaF(3):Yb,Tm upconversion nanoparticles (UCNPs@SiO(2)-FA) with high La content in a single particle were strategically designed and prepared for simultaneously targeting dual-modality imaging of upconversion luminescence (UCL) and X-ray computed tomography (CT). LaF(3) UCNPs were synthesized by a novel oleic acid (OA)/ionic liquid (IL) two-phase system. Afterward, a folic acid molecule was covalently anchored on the surface of UCNPs with a silane coupling agent. The UCNPs@SiO(2)-FA exhibits good stability, water dispersibility and solubility, low cytotoxicity, good biocompatibility, highly selective targeting, excellent X-ray attenuation, and UCL emission under excitation at 980 nm. In vivo UCL and CT images of mice show the UCNPs@SiO(2)-FA can be used in targeting dual-modality imaging. These results suggest that the as-prepared nanoprobe is a good candidate with excellent imaging and targeting ability for targeting dual-modality imaging of UCL and CT.