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Background: Next-generation sequencing (NGS) is fundamental to the current biological and biomedical research. Construction of sequencing library is a key step of NGS. Therefore, various library construction methods have been explored. However, the current methods are still limited by some shortcomings. Results: This study developed a new NGS library construction method, Single strand Adaptor Library Preparation (SALP), by using a novel single strand adaptor (SSA). SSA is a double-stranded oligonucleotide with a 3′ overhang of 3 random nucleotides, which can be efficiently ligated to the 3′ end of single strand DNA by T4 DNA ligase. SALP can be started with any denatured DNA fragments such as those sheared by Tn5 tagmentation, enzyme digestion and sonication. When started with Tn5-tagmented chromatin, SALP can overcome a key limitation of ATAC-seq and become a high-throughput NGS library construction method, SALP-seq, which can be used to comparatively characterize the chromatin openness state of multiple cells unbiasly. In this way, this study successfully characterized the comparative chromatin openness states of four different cell lines, including GM12878, HepG2, HeLa and 293T, with SALP-seq. Similarly, this study also successfully characterized the chromatin openness states of HepG2 cells with SALP-seq by using 105 to 500 cells. Conclusions: This study developed a new NGS library construction method, SALP, by using a novel kind of single strand adaptor (SSA), which should has wide applications in the future due to its unique performance. [ABSTRACT FROM AUTHOR]

Background: In the active shape model framework, principal component analysis (PCA) based statistical shape models (SSMs) are widely employed to incorporate high-level a priori shape knowledge of the structure to be segmented to achieve robustness. A crucial component of building SSMs is to establish shape correspondence between all training shapes, which is a very challenging task, especially in three dimensions.Methods: We propose a novel mesh-to-volume registration based shape correspondence establishment method to improve the accuracy and reduce the computational cost. Specifically, we present a greedy algorithm based deformable simplex mesh that uses vector field convolution as the external energy. Furthermore, we develop an automatic shape initialization method by using a Gaussian mixture model based registration algorithm, to derive an initial shape that has high overlap with the object of interest, such that the deformable models can then evolve more locally. We apply the proposed deformable surface model to the application of femur statistical shape model construction to illustrate its accuracy and efficiency.Results: Extensive experiments on ten femur CT scans show that the quality of the constructed femur shape models via the proposed method is much better than that of the classical spherical harmonics (SPHARM) method. Moreover, the proposed method achieves much higher computational efficiency than the SPHARM method.Conclusions: The experimental results suggest that our method can be employed for effective statistical shape model construction. [ABSTRACT FROM AUTHOR]

Background Iron nanoparticles (FeNPs) have attracted increasing attention over the past two decades owing to their promising application as biomedical agents. However, to ensure safe application, their potential nanotoxicity should be carefully and thoroughly evaluated. Studies on the effects of FeNPs on cells at the transcriptomic level will be helpful for identifying any potential nanotoxicity of FeNPs and providing valuable mechanistic insights into various FeNPs-induced nanotoxicities. Results This study investigated the effects of an 11-nm dimercaptosuccinic acid-coated magnetite nanoparticle on the gene expression profiles of two human cell lines, THP-1 and HepG2. It was found that the expression of hundreds of genes was significantly changed by a 24-h treatment with the nanoparticles at two doses, 50 μg/mL and 100 μg/mL, in the two cell types. By identifying the differentially expressed genes and annotating their functions, this study characterized the general and cell-specific effects of the nanoparticles on two cell types at the gene, biological process and pathway levels. At these doses, the overall effects of the nanoparticle on the THP-1 cells were the induction of various responses and repression of protein translation, but in the HepG2 cells, the main effects were the promotion of cell metabolism, growth and mobility. In combination with a previous study, this study also characterized the common genes, biological processes and pathways affected by the nanoparticle in two human and mouse cell lines and identified Id3 as a nanotoxicity biomarker of the nanoparticle. Conclusion The studied FeNPs exerted significant effects on the gene expression profiles of human cells. These effects were highly dependent on the innate biological functions of cells, i.e., the cell types. However, cells can also show some cell type-independent effects such as repression of Id3 expression. Id3 can be used as a nanotoxicity biomarker for iron nanoparticles. [ABSTRACT FROM AUTHOR]

Vessel centerline detection is very important in many medical applications. In the noise and low-contrast regions, most existing methods may only produce an incomplete and disconnected extraction of the vessel centerline if no user guidance is provided. A robust and automatic method is described for extraction of the vessel centerline. First, we perform small vessel enhancement by processing with a set of line detection filters, corresponding to the 13 orientations; for each voxel, the highest filter response is kept and added to the image. Second, we extract vessel centerline segment candidates by a thinning algorithm. Finally, a global optimization algorithm is employed for grouping and selecting vessel centerline segments. We validate the proposed method quantitatively on a number of synthetic data sets, the liver artery and lung vessel. Comparisons are made with two state-of-the-art vessel centerline extraction methods and manual extraction. The experiments show that our method is more accurate and robust that these state-of-the-art methods and is, therefore, more suited for automatic vessel centerline extraction. [ABSTRACT FROM AUTHOR]

The DNA-binding specificity of transcription factors (TFs) has broad impacts on cell physiology, cell development and in evolution. However, the DNA-binding specificity of most known TFs still remains unknown. The specificity of a TF protein is determined by its relative affinity to all possible binding sites. In recent years, the development of several in vitro techniques permits high-throughput determination of relative binding affinity of a TF to all possible k bp-long DNA sequences, thus greatly promoting the characterization of DNA-binding specificity of many known TFs. All DNA sequences that can be bound by a TF with various binding affinities form their DNA-binding profile (DBP). The DBP is important to generate an accurate DNA-binding model, identify all DNA-binding sites and target genes of TFs in the whole genome, and build transcription regulatory network. This study reviewed these techniques, especially two master techniques: double-stranded DNA microarray and systematic evolution of ligands by exponential enrichment in combination with parallel DNA sequencing techniques (SELEX-seq). [ABSTRACT FROM AUTHOR]

This work investigated the cell labeling of 12-nm meso-2,-3-dimercaptosuccinic acid (DMSA)-coated Fe3O4 magnetic nanoparticles with multiple mammalian cells. Six different cells, including RAW264.7, Hepa1-6, THP-1, HepG2, HeLa, and HL-7702, were treated with the nanoparticles at various concentrations (20~100 µg/mL) for different times (2~72 h), and the labeling effect was evaluated by observing the intracellular internalization of the nanoparticles with Prussian blue staining and measuring the corresponding cellular iron loading with colorimetric assay. The results demonstrated that the nanoparticles could label all cells studied. However, the labeling efficiency was not the same between different cells, which depended on the cell types, the nanoparticles' concentration, and the time of treating cells with the nanoparticles. In comparison, RAW264.7 was labeled more effectively than other cells at any concentration of the nanoparticles. The iron loading of RAW264.7 significantly increased with the concentration of the nanoparticles and the treatment time. However, both human liver cells (HepG2 and HL-7720) were labeled with the lowest iron loading. The measurement of cell viability revealed that the growth of all cells was not affected by the nanoparticles at a common in vivo application dose of iron nanoparticles (30 µg/mL), demonstrating that the nanoparticles have better biocompatability. [ABSTRACT FROM AUTHOR]

Background: In recent years, near-infrared fluorescence (NIRF)-labeled iron nanoparticles have been synthesized and applied in a number of applications, including the labeling of human cells for monitoring the engraftment process, imaging tumors, sensoring the in vivo molecular environment surrounding nanoparticles and tracing their in vivo biodistribution. These studies demonstrate that NIRF-labeled iron nanoparticles provide an efficient probe for cell labeling. Furthermore, the in vivo imaging studies show excellent performance of the NIR fluorophores. However, there is a limited selection of NIRF-labeled iron nanoparticles with an optimal wavelength for imaging around 800 nm, where tissue autofluorescence is minimal. Therefore, it is necessary to develop additional alternative NIRF-labeled iron nanoparticles for application in this area. Results: This study manufactured 12-nm DMSA-coated Fe3O4 nanoparticles labeled with a near-infrared fluorophore, IRDye800CW (excitation/emission, 774/789 nm), to investigate their applicability in cell labeling and in vivo imaging. The mouse macrophage RAW264.7 was labeled with IRDye800CW-labeled Fe3O4 nanoparticles at concentrations of 20, 30, 40, 50, 60, 80 and 100 μg/ml for 24 h. The results revealed that the cells were efficiently labeled by the nanoparticles, without any significant effect on cell viability. The nanoparticles were injected into the mouse via the tail vein, at dosages of 2 or 5 mg/kg body weight, and the mouse was discontinuously imaged for 24 h. The results demonstrated that the nanoparticles gradually accumulated in liver and kidney regions following injection, reaching maximum concentrations at 6 h post-injection, following which they were gradually removed from these regions. After tracing the nanoparticles throughout the body it was revealed that they mainly distributed in three organs, the liver, spleen and kidney. Real-time live-body imaging effectively reported the dynamic process of the biodistribution and clearance of the nanoparticles in vivo. Conclusion: IRDye800CW-labeled Fe3O4 nanoparticles provide an effective probe for cell-labeling and in vivo imaging. [ABSTRACT FROM AUTHOR]