Systematic Comparison of Computational Tools for Sanger Sequencing-Based Genome Editing Analysis.

Successful genome editing depends on the cleavage efficiency of programmable nucleases (PNs) such as the CRISPR-Cas system. Various methods have been developed to assess the efficiency of PNs, most of which estimate the occurrence of indels caused by PN-induced double-strand breaks. In these methods, PN genomic target sites are amplified through PCR, and the resulting PCR products are subsequently analyzed using Sanger sequencing, high-throughput sequencing, or mismatch detection assays.

CRISPR-Cas9-Mediated Genome Modifications in Zebrafish.

CRISPR-Cas9 genome editing technology has been successfully applied to generate various genetic modifications in zebrafish. The CRISPR-Cas9 system, which originally consisted of three components, CRISPR RNA (crRNA), trans-activating crRNA (tracrRNA), and Cas9, efficiently induces DNA double-strand breaks (DSBs) at targeted genomic loci, often resulting in frameshift-mediated target gene disruption (knockout). However, it remains difficult to perform the targeted integration of exogenous DNA fragments (knock-in) with CRISPR-Cas9.

Corrigendum: A Glycosylphosphatidylinositol-Anchored α-Amylase Encoded by Contributes to a Decrease in the Molecular Mass of Cell Wall α-1,3-Glucan in .

[This corrects the article DOI: 10.3389/ffunb.2021.

Key sequence features of CRISPR RNA for dual-guide CRISPR-Cas9 ribonucleoprotein complexes assembled with wild-type or HiFi Cas9.

Specific sequence features of the protospacer and protospacer-adjacent motif (PAM) are critical for efficient cleavage by CRISPR-Cas9, but current knowledge is largely derived from single-guide RNA (sgRNA) systems assessed in cultured cells. In this study, we sought to determine gRNA sequence features of a more native CRISPR-Cas9 ribonucleoprotein (RNP) complex with dual-guide RNAs (dgRNAs) composed of crRNA and tracrRNA, which has been used increasingly in recent CRISPR-Cas9 applications, particularly in zebrafish. Using both wild-type and HiFi SpCas9, we determined on-target cleavage efficiencies of 51 crRNAs in zebrafish embryos by assessing indel occurrence.

Improved recombinant protein production in Aspergillus oryzae lacking both α-1,3-glucan and galactosaminogalactan in batch culture with a lab-scale bioreactor.

Filamentous fungi are used as production hosts for various commercially valuable enzymes and chemicals including organic acids and secondary metabolites. We previously revealed that α-1,3-glucan and galactosaminogalactan (GAG) contribute to hyphal aggregation in the industrial fungus Aspergillus oryzae, and that production of recombinant protein in shake-flask culture is higher in a mutant lacking both α-1,3-glucan and GAG (AGΔ-GAGΔ) than in the parental strain. Here, we compared the productivity of the wild type, AGΔ-GAGΔ, and mutants lacking α-1,3-glucan (AGΔ) or GAG (GAGΔ) in batch culture with intermittent addition of glucose in a 5-L lab-scale bioreactor.

Bone union status of all osteotomy sites one year after curved periacetabular osteotomy based on computed tomography.

Background: Curved periacetabular osteotomy (CPO) is a joint-preservation surgery to treat acetabular dysplasia. It is performed via an anterior approach with the osteotomy of the anterosuperior iliac spine (ASIS). One of the complications associated with CPO includes non-union of the osteotomy sites.

Efficient CRISPR-Cas9-Mediated Knock-In of Composite Tags in Zebrafish Using Long ssDNA as a Donor.

Despite the unprecedented gene editing capability of CRISPR-Cas9-mediated targeted knock-in, the efficiency and precision of this technology still require further optimization, particularly for multicellular model organisms, such as the zebrafish (). Our study demonstrated that an ∼200 base-pair sequence encoding a composite tag can be efficiently "knocked-in" into the zebrafish genome using a combination of the CRISPR-Cas9 ribonucleoprotein complex and a long single-stranded DNA (lssDNA) as a donor template. Here, we targeted the , , and genes to evaluate the knock-in efficiency of lssDNA donors with different structures in somatic cells of injected embryos and for their germline transmission.

Magnetic Resonance Imaging Assessment of Abductor Muscles Shortly After Curved Periacetabular Osteotomy.

Background: Curved periacetabular osteotomy (CPO) is performed via an anterior approach without detachment of the hip abductor muscles. This study aimed to evaluate the abductor muscle status shortly after CPO on magnetic resonance imaging (MRI).

Methods: We prospectively evaluated 38 hips in 38 patients 1 week and 3 months after CPO between October 2017 and July 2019.

HiBiT-qIP, HiBiT-based quantitative immunoprecipitation, facilitates the determination of antibody affinity under immunoprecipitation conditions.

The affinity of an antibody for its antigen serves as a critical parameter for antibody evaluation. The evaluation of antibody-antigen affinity is essential for a successful antibody-based assay, particularly immunoprecipitation (IP), due to its strict dependency on antibody performance. However, the determination of antibody affinity or its quantitative determinant, the dissociation constant (K), under IP conditions is difficult.

Preparation of Ultraviolet Curing Type Silicone Rubbers Containing Mesoporous Silica Fillers.

Here we have been focusing on mesoporous silica (MPS) as inorganic filler material to improve the mechanical strength of silicone rubbers. The MPS particles are more effective in reducing the coefficient of thermal expansion (CTE) and hardening silicone rubber composites when compared to commercially available nonporous silica particles. In this study, we utilize ultraviolet curing type silicone rubbers and prepare MPS composites according to a simple single-step method.

Cooperation of Sall4 and Sox8 transcription factors in the regulation of the chicken Sox3 gene during otic placode development.

To elucidate the transcriptional regulation that underlies specification of the otic placode, we investigated the Sox3 downstream enhancer Otic1 of the chicken, the activity of which is restricted to and distributed across the entire otic placode. The 181-bp Otic1 enhancer sequence was dissected into a 68-bp minimal activating sequence, which exhibited dimer enhancer activity in the otic placode and cephalic neural crest, and this was further reduced to a 25-bp Otic1 core sequence, which also showed octamer enhancer activity in the same regions. The Otic1 core octamer was activated by the combined action of Sall4 and the SoxE transcription factors (TFs) Sox8 or Sox9.

Development of hyper osmotic resistant CHO host cells for enhanced antibody production.

Cell culture platform processes are generally employed to shorten the duration of new product development. A fed-batch process with continuous feeding is a conventional platform process for monoclonal antibody production using Chinese hamster ovary (CHO) cells. To establish a simplified platform process, the feeding method can be changed from continuous feed to bolus feed.

Hydrogels Containing Prussian Blue Nanoparticles Toward Removal of Radioactive Cesium Ions.

Recent reports have demonstrated the practical application of Prussian blue (PB) nanoparticles toward environmental clean-up of radionuclide 173Cs. Herein, we prepared a large amount of PB nanoparticles by mixing both iron(III) chloride and sodium ferrocyanide hydrate as starting precursors. The obtained PB nanoparticles show a high surface area (440 m2.

Regulation of trunk neural crest delamination by δEF1 and Sip1 in the chicken embryo.

The vertebrate Zfhx1 transcription factor family comprises δEF1 and Sip1, which bind to CACCT-containing sequences and act as transcriptional repressors. It has been a longstanding question whether these transcription factors share the same regulatory functions in vivo. It has been shown that neural crest (NC) delamination depends on the Sip1 activity at the cranial level in mouse and chicken embryos, and it remained unclear how NC delamination is regulated at the trunk level.

Sodium Hydroxide Activated Nanoporous Carbons Based on Lapsi Seed Stone.

Nanoporous activated carbons (ACs) were prepared from Lapsi (Choerospondias axillaris) seed powder by chemical activation with sodium hydroxide (NaOH) at different NaOH impregnation ratios. The prepared ACs were characterized by Fourier transform-infrared (FTIR) spectroscopy, Raman scattering, X-ray diffraction (XRD), and scanning electron microscopy (SEM). Semi-quantitative information on the surface properties was obtained by estimating iodine number.

Asymmetric Supercapacitors Using 3D Nanoporous Carbon and Cobalt Oxide Electrodes Synthesized from a Single Metal-Organic Framework.

Nanoporous carbon and nanoporous cobalt oxide (Co3O4) materials have been selectively prepared from a single metal-organic framework (MOF) (zeolitic imidazolate framework, ZIF-67) by optimizing the annealing conditions. The resulting ZIF-derived carbon possesses highly graphitic walls and a high specific surface area of 350 m(2)·g(-1), while the resulting ZIF-derived nanoporous Co3O4 possesses a high specific surface area of 148 m(2)·g(-1) with much less carbon content (1.7 at%).

Preparation of a platinum electrocatalyst by coaxial pulse arc plasma deposition.

We have developed a new method of preparing Pt electrocatalysts through a dry process. By coaxial pulse arc plasma deposition (CAPD), highly ionized metal plasma can be generated from a target rod without any discharged gases, and Pt nanoparticles can be deposited on a carbon support. The small-sized Pt nanoparticles are distributed over the entire carbon surface.

Mesoporous silica particles as topologically crosslinking fillers for poly(N-isopropylacrylamide) hydrogels.

Here it is demonstrated that mesoporous silicas (MPSs) can be used as effective "topological crosslinkers" for poly(N-isopropylacrylamide) (PNIPA) hydrogels to improve the mechanical property. Three-dimensional bicontinuous mesporous silica is found to effectively reinforce the PNIPA hydrogels, as compared to nonporous silica and two-dimensional hexagonally ordered mesoporous silica.

Diffuse-type tenosynovial giant cell tumor with t(1;17)(p13;p13) and trisomy 5.

Diffuse-type tenosynovial giant cell tumor (TSGCT) is a locally aggressive neoplasm that primarily affects the synovium and tendon sheath in young adults. Rearrangement of chromosome band 1p13 is now considered a characteristic genetic feature of TSGCT, with the most frequent chromosomal alteration t(1;2)(p13;q37). Here, we describe a unique cytogenetic finding of diffuse-type TSGCT arising in the ankle of an 18-year-old woman.

Atypical lipomatous tumor with structural rearrangements involving chromosomes 3 and 8.

Atypical lipomatous tumor (ALT) is an intermediate (locally aggressive) mesenchymal neoplasm with the potential to dedifferentiate to higher grades over time. It is cytogenetically characterized by the presence of one or more supernumerary ring and giant marker chromosomes. These abnormal chromosomes invariably contain amplified sequences derived from the 12q14-15 region.

Controlled crystallization of cyano-bridged Cu-Pt coordination polymers with two-dimensional morphology.

Two-dimensional (2D) coordination polymers (CPs) have a highly accessible surface area that permits guest molecules to effectively access the micropores in the CPs. Here we report a bottom-up synthesis of 2D cyano-bridged Cu-Pt CP nanoflakes using trisodium citrate as a chelating agent, which controls the nucleation rate and the crystal growth. The lateral sizes of the CP nanoflakes are controlled by changing the amount of trisodium citrate used.

Selective expansion of donor-derived regulatory T cells after allogeneic bone marrow transplantation in a patient with IPEX syndrome.

IPEX syndrome is a rare and fatal disorder caused by absence of regulatory T cells (Tregs) due to congenital mutations in the Forkhead box protein 3 gene. Here, we report a patient with IPEX syndrome treated with RIC followed by allogeneic BMT from an HLA-matched sibling donor. We could achieve engraftment and regimen-related toxicity was well tolerated.

Nano-analysis of DNA conformation changes induced by transcription factor complex binding using plasmonic nanodimers.

The plasmon resonant wavelength for a pair of gold nanoparticles, or gold nanodimer, increases inversely with the gap distance between the two nanoparticles. Taking advantage of this property, we performed nanoscale measurements of DNA conformation changes induced by transcription factor binding. Gold nanoparticles were bridged by double-stranded DC5 DNA that included binding sequences for the transcription factors SOX2 and PAX6, which interact on the DC5 enhancer sequence and activate transcription.