Unexpected CRISPR off-target mutation pattern in vivo are not typically germline-like [preprint]

A computationally evolutionary investigation was performed to re-analyze the WGS data of the two studies published in Nature Methods (2015, 2017) with opposite conclusions on CRISPR off-target mutations. Our analysis concluded that the so-called unexpected SNVs pattern obtained by the study of Schaefer et al. are not typically germline-like. Some of unusual and unidentified mutations may arise, but the real reasons remain to be explored. Based on the available data and a direct comparison of the two studies, we presented two possible reasons and future re-analysis directions that may contribute to such different conclusions. To characterize the authentic CRISPR-mediated mutations, we are required to have appropriate controls to rule out other sources of mutations, which will be needed for benchmarking of targeting safety of CRISPR-based gene therapy

Novel immune–risk score of gastric cancer: A molecular prediction model combining the value of immune–risk status and chemosensitivity

Abstract Gastric cancer is still one of the most common and deadly malignancies in the world. Not all patients could benefit from chemotherapy or chemoradiotherapy due to tumor heterogeneity. Therefore, identifying different subgroups of patients is an important trend for obtaining more effective responses. However, few molecular classifications associated with chemosensitivity are based on immune–risk status. In this study, we obtained six key immune–related genes. Using these genes, we constructed a molecular model related to immune–risk status and calculated an individual immune–risk score. The score showed great efficiency and stability in predicting prognosis and identifying different subgroups where persons could benefit from postoperative adjuvant therapy. The patients could be divided into different risk groups based on the immune–related score. For patients in the low–risk group, both postoperative chemoradiotherapy and chemotherapy could significantly improve prognosis on overall survival (OS) and disease–free survival (DFS) (DFS, P < 0.001 and P = 0.041, respectively; OS, P < 0.001, P = 0.006, respectively) and chemoradiotherapy was significantly superior than simple chemotherapy (DFS, P = 0.031; OS, P = 0.027). For patients with an intermediate–risk score, postoperative chemoradiotherapy showed a statistically significant survival advantage over no anticancer treatment (P = 0.004 and P = 0.002, respectively), while chemotherapy did not. Compared with no adjuvant treatment, neither postoperative chemoradiotherapy nor chemotherapy made significant difference for patients in the high–risk group. Combining the value of immune–risk status and chemosensitivity, the immune–risk score could not only offer us prognostic evaluation and adjuvant treatment guidance, but also improve our understanding about the binding point between chemotherapy or chemoradiotherapy and the immune system, which may be helpful for further expanding the application of immunotherapy

Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation

The white-blotched river stingray (Potamotrygon leopoldi) is a cartilaginous fish native to the Xingu River, a tributary of the Amazon River system. As a rare freshwater-dwelling cartilaginous fish in the Potamotrygonidae family in which no member has the genome sequencing information available, P. leopoldi provides the evolutionary details in fish phylogeny, niche adaptation, and skeleton formation. In this study, we present its draft genome of 4.11 Gb comprising 16,227 contigs and 13,238 scaffolds, with contig N50 of 3937 kb and scaffold N50 of 5675 kb in size. Our analysis shows that P. leopoldi is a slow-evolving fish that diverged from elephant sharks about 96 million years ago. Moreover, two gene families related to the immune system (immunoglobulin heavy constant delta genes and T-cell receptor alpha/delta variable genes) exhibit expansion in P. leopoldi only. We also identified the Hox gene clusters in P. leopoldi and discovered that seven Hox genes shared by five representative fish species are missing in P. leopoldi. The RNA sequencing data from P. leopoldi and other three fish species demonstrate that fishes have a more diversified tissue expression spectrum when compared to mammals. Our functional studies suggest that lack of the gc gene encoding vitamin D-binding protein in cartilaginous fishes (both P. leopoldi and Callorhinchus milii) could partly explain the absence of hard bone in their endoskeleton. Overall, this genome resource provides new insights into the niche adaptation, body plan, and skeleton formation of P. leopoldi, as well as the genome evolution in cartilaginous fishes

Theoretical and experimental bases for the equivalent circuit model for interpretation of silty soil at different temperatures

The exploitation of underground space is accompanied by complex geotechnical problems. The development of electromagnetic exploration technology provides a new perspective for preventing and avoiding these problems. In this work, electrochemical impedance spectroscopy (EIS) was used to test the single-phase and mixed-phase medium. Based on the unsaturated soil theory and the dual-water conductivity theory, an equivalent circuit model to describe the electrochemical characteristics and microstructure of silty soil with temperature changes through comparative research. The results indicate that the resistance of near-water layer is not affected by temperature, the resistance of silty soil increases mainly results from the influence of the far-water layer until which increases significantly after freezing. The capacitance change of silty soil is mainly affected by the slowing down of the orientation movement of polar molecules in the far-water layer. Based on the fitting data, a mathematical model for calculating the unfrozen water content of frozen soil was proposed, which reasonably verified the relationship between the unfrozen water content and electrical resistance. By improving the testing conditions of electrochemical impedance spectroscopy, this method may provide new insights for future research of soil electromagnetic testing technology

A Novel Pak1/ATF2/miR-132 Signaling Axis Is Involved in the Hematogenous Metastasis of Gastric Cancer Cells

We, along with others, have shown previously that P21-activated kinase 1 (Pak1) plays a pivotal role in gastric cancer progression and metastasis. However, whether Pak1 controls gastric cancer metastasis by regulating microRNAs (miRNAs) has never been explored. Here, we report a novel mechanism of Pak1 in tumor metastasis. A detailed examination revealed that Pak1 interacts with and phosphorylates the serine 62 residue of ATF2 and then blocks its translocation into the nucleus. We also confirmed that ATF2 binds to the promoter of miR-132 and tightly regulates its transcription, thus explaining the regulatory mechanism of miR-132 by Pak1. miR-132 also significantly reduced cell adhesion, migration, and invasion of gastric cancer cells in vitro and significantly prevented tumor metastasis in vivo. miR-132 specifically inhibited hematogenous metastasis, but not lymph node or implantation metastases. In order to further delineate the effects of the Pak1/ATF2/miR-132 cascade on gastric cancer progression, we identified several targets of miR-132 using a bioinformatics TargetScan algorithm. Notably, miR-132 reduced the expression of CD44 and fibronectin1 (FN1), and such inhibition enabled lymphocytes to home in on gastric cancer cells and induce tumor apoptosis. Taken together, our studies establish a novel cell-signaling pathway and open new possibilities for therapeutic intervention of gastric cancer. Keywords: p21-activated kinase 1, activating transcription factor-2, miR-132, hematogenous metastasi

Liver fat volume fraction measurements based on multi-material decomposition algorithm in patients with nonalcoholic fatty liver disease: the influences of blood vessel, location, and iodine contrast

Abstract Background In recent years, spectral CT-derived liver fat quantification method named multi-material decomposition (MMD) is playing an increasingly important role as an imaging biomarker of hepatic steatosis. However, there are various measurement ways with various results among different researches, and the impact of measurement methods on the research results is unknown. The aim of this study is to evaluate the reproducibility of liver fat volume fraction (FVF) using MMD algorithm in nonalcoholic fatty liver disease (NAFLD) patients when taking blood vessel, location, and iodine contrast into account during measurement. Methods This retrospective study was approved by the institutional ethics committee, and the requirement for informed consent was waived because of the retrospective nature of the study. 101 patients with NAFLD were enrolled in this study. Participants underwent non-contrast phase (NCP) and two-phase enhanced CT scanning (late arterial phase (LAP) and portal vein phase (PVP)) with spectral mode. Regions of interest (ROIs) were placed at right posterior lobe (RPL), right anterior lobe (RAL) and left lateral lobe (LLL) to obtain FVF values on liver fat images without and with the reference of enhanced CT images. The differences of FVF values measured under different conditions (ROI locations, with/without enhancement reference, NCP and enhanced phases) were compared. Friedman test was used to compare FVF values among three phases for each lobe, while the consistency of FVF values was assessed between each two phases using Bland–Altman analysis. Results Significant difference was found between FVF values obtained without and with the reference of enhanced CT images. There was no significant difference about FVF values obtained from NCP images under the reference of enhanced CT images between any two lobes or among three lobes. The FVF value increased after the contrast injection, and there were significant differences in the FVF values among three scanning phases. Poor consistencies of FVF values between each two phases were found in each lobe by Bland–Altman analysis. Conclusion MMD algorithm quantifying hepatic fat was reproducible among different lobes, while was influenced by blood vessel and iodine contrast

Electric field control for energy efficient domain wall injection

Domain wall injection by electric means is an energy exhausting process. This process is conventionally carried out by sending a current pulse through a stripline which generates an Oersted field to locally switch the magnetization in a magnetic wire. In this work, the magnetic properties of the device were modulated by electric control to lower the required current density for DW injection. The proposed DW injection device employs a Hall cross structure which simplifies the device fabrication process and allows a larger Oersted field to be generated at the domain wall injection region. Electrical pulses of 50 ns were sent through the Hall bar to inject domain walls. The formation of the resulting domain walls was detected electrically using the Hall resistance and optically by Kerr microscopy. The results show that the required current density for injection of domain walls is reduced by ∼20% with an applied electric field of +250 MV/m on the Hall cross structure.Agency for Science, Technology and Research (A*STAR)National Research Foundation (NRF)The work was supported by the Singapore National Research Foundation, Prime Minister’s Office under a Competitive Research Programme (Non-volatile Magnetic Logic and Memory Integrated Circuit Devices, NRF-CRP9-2011-01), and an Industry-IHL Partnership Program (NRF2015-IIP001-001). The supports from a RIE2020 ASTAR AME IAF-ICP Grant (No. I1801E0030) and an ASTAR AME Programmatic Grant (No. A1687b0033) is also acknowledged. WSL is a member of the Singapore Spintronics Consortium (SG-SPIN)

Self-assembled short peptides: Recent advances and strategies for potential pharmaceutical applications

Self-assembled short peptides have intrigued scientists due to the convenience of synthesis, good biocompatibility, low toxicity, inherent biodegradability and fast response to change in the physiological environment. Therefore, it is necessary to present a comprehensive summary of the recent advances in the last decade regarding the construction, route of administration and application of self-assembled short peptides based on the knowledge on their unique and specific ability of self-assembly. Herein, we firstly explored the molecular mechanisms of self-assembly of short peptides, such as non-modified amino acids, as well as Fmoc-modified, N-functionalized, and C-functionalized peptides. Next, cell penetration, fusion, and peptide targeting in peptide-based drug delivery were characterized. Then, the common administration routes and the potential pharmaceutical applications (drug delivery, antibacterial activity, stabilizers, imaging agents, and applications in bioengineering) of peptide drugs were respectively summarized. Last but not least, some general conclusions and future perspectives in the relevant fields were briefly listed. Although with certain challenges, great opportunities are offered by self-assembled short peptides to the fascinating area of drug development