(Tn5-)fish-based imaging in the era of 3D/spatial genomics

3D genomics mainly focuses on the 3D position of single genes at the cell level, while spatial genomics focuses more on the tissue level. In this exciting new era of 3D/spatial genomics, half-century old FISH and its derivative methods, including Tn5-FISH, play important roles. In this review, we introduce the Tn5-FISH we developed recently, and present six different applications published by our collaborators and us, based on (Tn5-)FISH, which can be either general BAC clone-based FISH or Tn5-FISH. In these interesting cases, (Tn5-)FISH demonstrated its vigorous ability of targeting sub-chromosomal structures across different diseases and cell lines (leukemia, mESCs (mouse embryonic stem cells), and differentiation cell lines). Serving as an effective tool to image genomic structures at the kilobase level, Tn5-FISH holds great potential to detect chromosomal structures in a high-throughput manner, thus bringing the dawn for new discoveries in the great era of 3D/spatial genomics

Interpolatory Catmull-Clark volumetric subdivision over unstructured hexahedral meshes for modeling and simulation applications

International audienceVolumetric modeling is an important topic for material modeling and isogeometric simulation. In this paper, two kinds of interpolatory Catmull-Clark volumetric subdivision approaches over unstructured hexahedral meshes are proposed based on the limit point formula of Catmull-Clark subdivision volume. The basic idea of the first method is to construct a new control lattice, whose limit volume by the CatmullClark subdivision scheme interpolates vertices of the original hexahedral mesh. The new control lattice is derived by the local push-back operation from one CatmullClark subdivision step with modified geometric rules. This interpolating method is simple and efficient, and several shape parameters are involved in adjusting the shape of the limit volume. The second method is based on progressive-iterative approximation using limit point formula. At each iteration step, we progressively modify vertices of an original hexahedral mesh to generate a new control lattice whose limit volume interpolates all vertices in the original hexahedral mesh. The convergence proof of the iterative process is also given. The interpolatory subdivision volume has C 2-smoothness at the regular region except around extraordinary vertices and edges. Furthermore, the proposed interpolatory volumetric subdivision methods can be used not only for geometry interpolation, but also for material attribute interpolation in the field of volumetric material modeling. The application of the proposed volumetric subdivision approaches on isogeometric analysis is also given with several examples

Structural and evolutionary characteristics of dynamin-related GTPase OPA1

OPA1 is a dynamin-related GTPase that controls mitochondrial fusion, cristae remodeling, energetics and mtDNA maintenance. However, the molecular architecture of OPA1 is poorly understood. Here we modeled the structure of human OPA1 by the threading approach. We found that the C-terminal region of the OPA1 protein had multiple functional domains, while the N-terminal region was rich in alpha helices and did not include specific domains. For the short soluble forms of OPA1, we observed that there were obvious hydrophobic regions near the two cleavage sites and the N-terminal was positively charged after cleavage. The blue native analysis revealed that the protein could form stable homodimers. In addition, the evolutionary conservation of the C-terminal region, where most of the known mutated disease-related sites were located, was significantly higher than that of the N-terminal region. These findings provided new insights into the structure and biochemical function of OPA1

MYB75 phosphorylation by MPK4 is required for light-induced anthocyanin accumulation in arabidopsis

Light is a major environmental cue affecting various physiological and metabolic processes in plants. Although plant photoreceptors are well characterized, the mechanisms by which light regulates downstream responses are less clear. In Arabidopsis thaliana, the accumulation of photoprotective anthocyanin pigments is light dependent, and the R2R3 MYB transcription factor MYB75/PAP1 regulates anthocyanin accumulation. Here, we report that MYB75 interacts with and is phosphorylated by MAP KINASE4 (MPK4). Their interaction is dependent on MPK4 kinase activity and is required for full function of MYB75. MPK4 can be activated in response to light and is involved in the light-induced accumulation of anthocyanins. We show that MPK4 phosphorylation of MYB75 increases its stability and is essential for light-induced anthocyanin accumulation. Our findings reveal an important role for a MAPK pathway in light signal transduction

DataSheet1_Minoxidil delivered via a stem cell membrane delivery controlled release system promotes hair growth in C57BL/6J mice.docx

Objective: Umbilical cord-derived mesenchymal stem cell membrane-loaded minoxidil (MXD) nanoparticles (STCM-MXD-NPs) were prepared to investigate their effects on hair growth in C57BL/6J mice.Methods: STCM-MXD-NPs were obtained by freeze-thawing and differential centrifugation, and their effects on hair growth were evaluated using C57BL/6J mice. The mRNA and protein expression levels of vascular endothelial growth factor (VEGF) and insulin-like growth factor-1 (IGF-1) were detected by real-time polymerase chain reaction and enzyme-linked immunosorbent assays, respectively. Protein expression levels of marker of proliferation Ki-67 (MKI67) and β-catenin (CTNNB) in skin tissue were detected by immunohistochemistry.Results: STCM-MXD-NPs improved MXD solubility. They released the drug slowly, increasing its transdermal properties, accumulation in the skin, and content in the hair bulb tissues with a better efficacy than that of ordinary MXD. Moreover, STCM-MXD-NPs significantly upregulated the mRNA and protein levels of VEGF and IGF-1 and promoted the protein expression of MKI67 and CTNNB in mouse skin tissues, promoting mouse hair growth.Conclusion: Stem cell membrane-loaded MXD nanoparticles with slow-release properties increased MXD accumulation in the skin by improving its transdermal properties, increasing VEGF, IGF-1, MKI67, and CTNNB expression levels and promoting hair growth in C57BL/6J mice.</p

Evaluation of next-generation sequencing versus next-generation flow cytometry for minimal-residual-disease detection in Chinese patients with multiple myeloma

Abstract Purpose To evaluate the efficacy of next-generation sequencing (NGS) in minimal-residual-disease (MRD) monitoring in Chinese patients with multiple myeloma (MM). Methods This study analyzed 60 Chinese MM patients. During MRD monitoring in these patients’ post-therapy, clonal immunoglobulin heavy chain (IGH) rearrangements were detected via NGS using LymphoTrack assays. MRD monitoring was performed using NGS or next-generation flow cytometry (NGF), and the results were compared. Additionally, the sensitivity and reproducibility of the NGS method were assessed. Results The MRD detection range of the NGS method was 10–6–10–1, which suggested good linearity, with a Pearson correlation coefficient of 0.985 and a limit of detection of 10–6. Intra- and inter-assay reproducibility analyses showed that NGS exhibited 100% reproducibility with low variability in clonal cells. At diagnosis, unique clones were found in 42 patients (70.0%) with clonal IGH rearrangements, which were used as clonality markers for MRD monitoring post-therapy. Comparison of NGS and NGF for MRD monitoring showed 79.1% concordance. No samples that tested MRD-positive via NGF were found negative via NGS, indicating the higher sensitivity of NGS. MRD could be detected using NGS in 6 of 7 samples before autologous hematopoietic stem-cell transplantation, and 5 of them tested negative post-transplantation. In contrast, the NGF method could detect MRD in only 1 sample pre-transplantation. Conclusion Compared with NGF, NGS exhibits higher sensitivity and reproducibility in MRD detection and can be an effective strategy for MRD monitoring in Chinese MM patients