BackgroundAberrant activation of the Wnt/β-catenin signaling pathway is frequently observed in colorectal cancer (CRC). β-catenin is the major Wnt signaling pathway effector and inactivation of adenomatous polyposis coli (APC) results in nuclear accumulation of β-catenin. It has been suggested that inactivation of APC plays an important role in activation of the Wnt/β-catenin pathway and in the progression of colorectal tumorigenesis. However, the mechanism through which APC mediates colorectal tumorigenesis is not understood. Increasing evidence suggests that the dysregulation of microRNAs (miRNAs) is involved in colorectal tumorigenesis. Although miR-494 has been reported as being an upregulated miRNA, the interplay between miR-494 and APC-mediated colorectal tumorigenesis progression remains unclear.MethodsThe expression of miR-494 in tissues from patients diagnosed with CRC was analyzed using a microarray and real-time PCR. The effects of miR-494 on cell proliferation and tumorigenesis in CRC cells were analyzed by flow cytometry, colony formation assays, BrdU incorporation assays, and CCK8 assays. The correlation between miR-494 expression and APC expression, as well as the mechanisms by which miR-494 regulates APC in CRC were also addressed.ResultsmiR-494 was significantly upregulated in CRC tissues, and this increase was negatively associated with APC expression. APC was confirmed to be a direct target of miR-494 in CRC. Furthermore, overexpression of miR-494 induced Wnt/β-catenin signaling by targeting APC, thus promoting CRC cell growth.ConclusionsThis study provides novel insights into the role of miR-494 in controlling CRC cell proliferation and tumorigenesis, and identifies miR-494 as a potential prognostic marker and therapeutic target.

CRISPR-based nucleic acid detection methods are reported to facilitate rapid and sensitive DNA detection. However, precise DNA detection at the single-base resolution and its wide applications including high-fidelity SNP genotyping remain to be explored. Here we develop a Cas12b-mediated DNA detection (CDetection) strategy, which shows higher sensitivity on examined targets compared with the previously reported Cas12a-based detection platform. Moreover, we show that CDetection can distinguish differences at the single-base level upon combining the optimized tuned guide RNA (tgRNA). Therefore, our findings highlight the high sensitivity and accuracy of CDetection, which provides an efficient and highly practical platform for DNA detection. Electronic supplementary material The online version of this article (10.1186/s13059-019-1742-z) contains supplementary material, which is available to authorized users.

Dear Editor, The novel coronavirus (CoV) disease termed COVID-19 (coronavirus disease-19) caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) 1 is causing a massive pandemic worldwide, threatening public health systems across the globe. During this ongoing COVID-19 outbreak, nucleic-acid detection has played an important role in early diagnosis 2. To date, four protocols based on CRISPR for detecting SARS-CoV-2 have been published 3-6. Using lateral flow protocols, RNA samples harboring more than 1 × 10 4-1 × 10 5 copies/mL (SHERLOCK) or 1 × 10 4 copies/mL (DETECTR) can be detected within 1 hour. In addition to these reported efforts, we have also established a SARS-CoV-2 detection protocol based on our previously reported platform-CDetection (Cas12bmediated DNA detection) 7. By combining sample treatment protocols and nucleic-acid amplification methods with CDetection, we have established an integrated viral nucleic-acid detection platform-CASdetec (CRISPRassisted detection). The detection limit of CASdetec for SARS-CoV-2 pseudovirus is 1 × 10 4 copies/mL, with no cross-reactivity observed. Here, we present our assay design and optimization process, which could provide guidance for future CRISPR-based nucleic-acid detection assay development and optimization. To optimize the output of fluorescence signal, we designed and synthesized poly-T fluorescence-quenchers of varying nucleotide lengths, including 4 nt, 5 nt, 7 nt, 12 nt, 17 nt, 22 nt, and 27 nt. Of all the lengths tried, the 7 nt

The prokaryotic CRISPR-Cas adaptive immune systems provide valuable resources to develop genome editing tools, such as CRISPR-Cas9 and CRISPR-Cas12a/Cpf1. Recently, CRISPR-Cas12b/C2c1, a distinct type V-B system, has been characterized as a dual-RNA-guided DNA endonuclease system. Though being active in vitro, its cleavage activity at endogenous genome remains to be explored. Furthermore, the optimal cleavage temperature of the reported Cas12b orthologs is higher than 40 °C, which is unsuitable for mammalian applications. Here, we report the identification of a Cas12b system from the Alicyclobacillus acidiphilus (AaCas12b), which maintains optimal nuclease activity over a wide temperature range (31 °C–59 °C). AaCas12b can be repurposed to engineer mammalian genomes for versatile applications, including single and multiplex genome editing, gene activation, and generation of gene mutant mouse models. Moreover, whole-genome sequencing reveals high specificity and minimal off-target effects of AaCas12b-meditated genome editing. Our findings establish CRISPR-Cas12b as a versatile tool for mammalian genome engineering.

The ground-state deformations of the Ge isotopes are investigated in the framework of Gogny-Hartree-Fock-Bogoliubov (HFB) and Skyrme Hartree-Fock plus pairing in the BCS approximation. Five different Skyrme parametrizations are used to explore the influence of different effective masses and spin-orbit models. There is generally good agreement for binding energies and deformations (total quadrupole moment, triaxiality) with experimental data where available (i.e., in the valley of stability). All calculations agree in predicting a strong tendency for triaxial shapes in the Ge isotopes with only a few exceptions due to neutron (sub-)shell closures. The frequent occurrence of energetically very close shape isomers indicates that the underlying deformation energy landscape is very soft. The general triaxial softness of the Ge isotopes is demonstrated in the fully triaxial potential energy surface. The differences between the forces play an increasing role with increasing neutron number. This concerns particularly the influence of the spin-orbit model, which has a visible effect on the trend of binding energies towards the drip line. Different effective mass plays an important role in predicting the quadrupole and triaxial deformations. The pairing strength only weakly affects binding energies and total quadrupole deformations, but considerably influences triaxiality.

CRISPR-Cas12a/Cpf1, a single RNA-guided endonuclease system, provides a promising tool for genome engineering. However, only three Cas12a orthologs have been employed for mammalian genome editing, and the editing efficiency as well as targeting coverage still requires improvements. Here, we harness six novel Cas12a orthologs for genome editing in human and mouse cells, some of which utilize simple protospacer adjacent motifs (PAMs) that remarkably increase the targeting range in the genomes. Moreover, we identify optimized CRISPR RNA (crRNA) scaffolds that can increase the genome editing efficiency of Cas12a.Electronic supplementary materialThe online version of this article (10.1186/s13059-019-1620-8) contains supplementary material, which is available to authorized users.

We search for nonlinear effects in nuclear giant resonances (GRs), in particular the isovector dipole and the isoscalar quadrupole modes. To that end, we employ a spectral analysis of time-dependent Hartree-Fock (TDHF) dynamics using Skyrme forces. Based on TDHF calculations over a wide range of excitation amplitudes, we explore the collectivity and degree of harmonic motion in these modes. Both GR modes turn out to be highly harmonic in heavy nuclei from A=100 on. There is no trace of a transition to irregular motion and multiple resonances are predicted. Slight anharmonicities are seen for light nuclei, particularly for 16 O. These are mainly caused by the spin-orbit splitting.

The tensor force is implemented into the time-dependent Hartree-Fock (TDHF) theory so that both exotic and stable collision partners, as well as their dynamics in heavy-ion fusion, can be described microscopically. The role of tensor force on fusion dynamics is systematically investigated for 40 Ca + 40 Ca, 40 Ca + 48 Ca, 48 Ca + 48 Ca, 48 Ca + 56 Ni, and 56 Ni + 56 Ni reactions which vary by the total number of spin-unsaturated magic numbers in target and projectile. A notable effect on fusion barriers and cross sections is observed by the inclusion of tensor force. The origin of this effect is analyzed. The influence of isoscalar and isovector tensor terms is investigated with the TIJ forces. These effects of tensor force in fusion dynamics are essentially attributed to the shift of lowlying vibration states of colliding partners and nucleon transfer in the asymmetric reactions. Our calculations of above-barrier fusion cross sections also show that tensor force does not significantly affect the dynamical dissipation at near-barrier energies.