Efficient gene editing in induced pluripotent stem cells enabled by an inducible adenine base editor with tunable expression.

The preferred method for disease modeling using induced pluripotent stem cells (iPSCs) is to generate isogenic cell lines by correcting or introducing pathogenic mutations. Base editing enables the precise installation of point mutations at specific genomic locations without the need for deleterious double-strand breaks used in the CRISPR-Cas9 gene editing methods. We created a bulk population of iPSCs that homogeneously express ABE8e adenine base editor enzyme under a doxycycline-inducible expression system at the AAVS1 safe harbor locus. These cells enabled fast, efficient and inducible gene editing at targeted genomic regions, eliminating the need for single-cell cloning and screening to identify those with homozygous mutations. We could achieve multiplex genomic editing by creating homozygous mutations in very high efficiencies at four independent genomic loci simultaneously in AAVS1-iABE8e iPSCs, which is highly challenging with previously described methods. The inducible ABE8e expression system allows editing of the genes of interest within a specific time window, enabling temporal control of gene editing to study the cell or lineage-specific functions of genes and their molecular pathways. In summary, the inducible ABE8e system provides a fast, efficient and versatile gene-editing tool for disease modeling and functional genomic studies.

Establishment and characterization of CSCRi006-A: an induced pluripotent stem cell line generated from a patient with Diamond-Blackfan Anemia (DBA) carrying ribosomal protein S19 (RPS19) mutation.

Diamond-Blackfan anemia (DBA) is a congenital hypoplastic anemia characterized by ineffective erythropoiesis. DBA is majorly caused by mutations in the ribosomal protein (RP) genes (Gadhiya and Wills in Diamond-Blackfan Anemia, https://www.statpearls.com/ ; 2023). A suitable disease model that yields a continuous supply of erythroid cells is required to study disease pathogenesis and drug discovery. Toward this, we reprogrammed dermal fibroblasts from a DBA patient with a heterozygous mutation c.22-23delAG in the RPS19 gene identified through exome sequencing. To generate induced pluripotent stem cells (iPSCs), we induced episomal expression of the reprogramming factors OTC3/4, L-MYC, LIN28, SOX2, and KLF4, and a p53 shRNA2. The DBA-iPSC line CSCRi006-A generated during this study was extensively characterized for its pluripotency and genome stability. The clone retained normal karyotype and showed high expression levels of pluripotency markers, OCT4, NANOG, SOX2, TRA-I-60, TRA-I-81, and SSEA4. It could differentiate into cells originating from all three germ cell layers, as identified by immunostaining for SOX17 (endoderm), Brachyury (mesoderm), and PAX6 (ectoderm). IPSCs provide a renewable source of cells for in vitro disease modeling. CSCRi006-A, a thoroughly characterized iPSC line carrying heterozygous RPS19 c.22-23delAG mutation, is a valuable cell line for the disease modeling of DBA. This iPSC line can be differentiated into different blood cell types to study the mechanisms of disease development and identify potential treatments.

Synthesis and Characterization of Highly Crystalline Bi-Functional Mn-Doped Zn2SiO4 Nanostructures by Low-Cost Sol-Gel Process.

Herein, we demonstrate a process for the synthesis of a highly crystalline bi-functional manganese (Mn)-doped zinc silicate (Zn2SiO4) nanostructures using a low-cost sol-gel route followed by solid state reaction method. Structural and morphological characterizations of Mn-doped Zn2SiO4 with variable doping concentration of 0.03, 0.05, 0.1, 0.2, 0.5, 1.0, and 2.0 wt% were investigated by using X-ray diffraction and high-resolution transmission electron microscopy (HR-TEM) techniques. HR-TEM-assisted elemental mapping of the as-grown sample was conducted to confirm the presence of Mn in Zn2SiO4. Photoluminescence (PL) spectra indicated that the Mn-doped Zn2SiO4 nanostructures exhibited strong green emission at 521 nm under 259 nm excitation wavelengths. It was observed that PL intensity increased with the increase of Mn-doping concentration in Zn2SiO4 nanostructures, with no change in emission peak position. Furthermore, magnetism in doped Zn2SiO4 nanostructures was probed by static DC magnetization measurement. The observed photoluminescence and magnetic properties in Mn-doped Zn2SiO4 nanostructures are discussed in terms of structural defect/lattice strain caused by Mn doping and the Jahn-Teller effect. These bi-functional properties of as-synthesized Zn2SiO4 nanostructures provide a new platform for their potential applications towards magneto-optical and spintronic and devices areas.

Efficient deletion of microRNAs using CRISPR/Cas9 with dual guide RNAs.

MicroRNAs (miRNAs) are short non-coding RNAs that play crucial roles in gene regulation, exerting post-transcriptional silencing, thereby influencing cellular function, development, and disease. Traditional loss-of-function methods for studying miRNA functions, such as miRNA inhibitors and sponges, present limitations in terms of specificity, transient effects, and off-target effects. Similarly, CRISPR/Cas9-based editing of miRNAs using single guide RNAs (sgRNAs) also has limitations in terms of design space for generating effective gRNAs. In this study, we introduce a novel approach that utilizes CRISPR/Cas9 with dual guide RNAs (dgRNAs) for the rapid and efficient generation of short deletions within miRNA genomic regions. Through the expression of dgRNAs through single-copy lentiviral integration, this approach achieves over a 90% downregulation of targeted miRNAs within a week. We conducted a comprehensive analysis of various parameters influencing efficient deletion formation. In addition, we employed doxycycline (Dox)-inducible expression of Cas9 from the AAVS1 locus, enabling homogeneous, temporal, and stage-specific editing during cellular differentiation. Compared to miRNA inhibitory methods, the dgRNA-based approach offers higher specificity, allowing for the deletion of individual miRNAs with similar seed sequences, without affecting other miRNAs. Due to the increased design space, the dgRNA-based approach provides greater flexibility in gRNA design compared to the sgRNA-based approach. We successfully applied this approach in two human cell lines, demonstrating its applicability for studying the mechanisms of human erythropoiesis and pluripotent stem cell (iPSC) biology and differentiation. Efficient deletion of miR-451 and miR-144 resulted in blockage of erythroid differentiation, and the deletion of miR-23a and miR-27a significantly affected iPSC survival. We have validated the highly efficient deletion of genomic regions by editing protein-coding genes, resulting in a significant impact on protein expression. This protocol has the potential to be extended to delete multiple miRNAs within miRNA clusters, allowing for future investigations into the cooperative effects of the cluster members on cellular functions. The protocol utilizing dgRNAs for miRNA deletion can be employed to generate efficient pooled libraries for high-throughput comprehensive analysis of miRNAs involved in different biological processes.

Bifunctional Application of Viologen-MoS2-CNT/Polythiophene Device as Electrochromic Diode and Half-Wave Rectifier.

A dual purpose solid state electrochromic diode has been fabricated using polythiophene (P3HT) and ethyl Viologen (EV), predoped with multiwalled carbon nanotubes (MWCNTs) and MoS2. The device has been designed by considering two important aspects, first, the complementary redox activity of P3HT and EV and second, the electron holding properties of MoS2 and MWCNTs. The latter is found to enhance the electrochromic performance of the solid state device. On the other hand, the complementary redox nature gives the asymmetric diodic I-V characteristic to the device which has been exploited to use the electrochromic device for rectification application. The MoS2 nanoflower and MWCNTs are synthesized by one-step hydrothermal and pyrolysis techniques and well characterized by scanning electron microscopy (SEM), X-ray analysis (XRD), and Raman spectroscopy. Electrochromic properties of the device have been studied in detail to reveal an improvement in device performance in terms of faster speed and high coloration efficiency and color contrast. In situ bias-dependent Raman spectroscopy has been performed to understand the operation mechanism of the electrochromic diode which reveals (bi-)polaron formation as a result of dynamic doping eventually leading to color change. A half-wave rectifier has been realized from the electrochromic diode which rectifies an AC voltage of frequency 1 Hz or less making it suitable for low frequency operation. The study opens a new possibility to design and fabricate multipurpose frequency selective electrochromic rectifiers.

Fano-Type Wavelength-Dependent Asymmetric Raman Line Shapes from MoS2 Nanoflakes.

Excitation wavelength-dependent Raman spectroscopy has been carried out to study electron-phonon interaction (Fano resonance) in multi-layered bulk 2H-MoS2 nano-flakes. The electron-phonon coupling is proposed to be caused due to interaction between energy of an excitonic quasi-electronic continuum and the discrete one phonon, first-order Raman modes of MoS2. It is proposed that an asymmetrically broadened Raman line shape obtained by 633 nm laser excitation is due to electron-phonon interaction whose electronic continuum is provided by the well-known A and B excitons. Typical wavelength-dependent Raman line shape has been observed, which validates and quantifies the Fano interaction present in the samples. The experimentally obtained Raman scattering data show very good agreement with the theoretical Fano-Raman line-shape functions and help in estimating the coupling strength. Values of the electron-phonon interaction parameter obtained, through line-shape fitting, for the two excitation wavelengths have been compared and shown to have generic Fano-type dependence on the excitation wavelength.

Gene Editing in Human Induced Pluripotent Stem Cells Using Doxycycline-Inducible CRISPR-Cas9 System.

Induced pluripotent stem cells (iPSCs) generated from patients are a valuable tool for disease modelling, drug screening, and studying the functions of cell/tissue-specific genes. However, for this research, isogenic iPSC lines are important for comparison of phenotypes in the wild type and mutant differentiated cells generated from the iPSCs. The advent of gene editing technologies to correct or generate mutations helps in the generation of isogenic iPSC lines with the same genetic background. Due to the ease of programming, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9-based gene editing tools have gained pace in gene manipulation studies, including investigating complex diseases like cancer. An iPSC line with drug inducible Cas9 expression from the Adeno-Associated Virus Integration Site 1 (AAVS1) safe harbor locus offers a controllable expression of Cas9 with robust gene editing. Here, we describe a stepwise protocol for the generation and characterization of such an iPSC line (AAVS1-PDi-Cas9 iPSC) with a doxycycline (dox)-inducible Cas9 expression cassette from the AAVS1 safe harbor site and efficient editing of target genes with lentiviral vectors expressing gRNAs. This approach with a tunable Cas9 expression that allows investigating gene functions in iPSCs or in the differentiated cells can serve as a versatile tool in disease modelling studies.

Growth and proliferation of caprine bone marrow mesenchymal stem cells on different culture media.

The growth and proliferation of mesenchymal stem cells are very sensitive in in vitro and a number of factors like media play a significant role in that context. In this study we assessed effect of different media on growth and proliferation of bone marrow derived mesenchymal stem cells (BMMSCs). The BMMSCs were isolated from caprine bone marrow and were subjected to magnetic activated cell sorting against CD90+, CD105+, CD271+and CD34- along with FC blocker. After characterisation, 2 × 104 cells were seeded in 12 well culture plates in four different media viz. MesenCult, MesenPRO, StemPro and complete DMEM (15 % FBS) to study their growth kinetic for 6 days from passage 0 (P0) to passage 3 (P3). The population doubling time (PDT) was derived from growth curve using logarithmic formula. The results showed that the BMMSCs growth and proliferation was highest in MesenCult media in P0 which varied significantly (p < 0.05) from rest of media and from P1 to P3, it was MesenPRO which yielded maximum cells (p < 0.05). The PDT was also in line with growth curve findings. In conclusion, the MesenPRO media had higher growth and proliferation rate from P1 to P3 although MesenCult had higher cell numbers in P0. In conclusion, the use of MesenPRO media could be a better option than conventional media when mesenchymal stem cells are used in clinical applications and other therapeutic purposes taking consideration to its higher growth and proliferation rate. And MesenCult would be a great option to harvest MSCs from P0.

Photocatalytic Degradation of Bisphenol-A using N, Co Codoped TiO2 Catalyst under Solar Light.

Advanced oxidation processes (AOPs) including heterogeneous photocatalysis has proven as one of the best technique for waste-water treatment. Photocatalytic process using semiconductor like TiO2 based heterogeneous photocatalysis is a promising method for the treatment of toxic pollutants. In the present study, visible-light photoactive cobalt and nitrogen co-doped TiO2 nanoparticles were synthesized via wet impregnation method. The photocatalysts were characterized using X-ray diffraction (XRD), Raman Spectra, Fourier Transform Infrared (FTIR) Spectroscopy, Scanning Electron Microscopy (SEM), Transmission Electron Microscope (TEM), UV-vis spectrophotometer and X-ray photoelectron spectrophotometer (XPS). The photocatalytic activitiy of prepared (N, Co)-codoped TiO2 on the mineralization of Bisphenol-A (BPA) under visible light irradiation was studied and the results were compared to commercial TiO2 (Degussa P25). The results demonstrated that 1.5% Co and 0.5% N - codoped TiO2 samples revealed higher activity than commercial TiO2. Total organic carbon (TOC) removal was observed to be 97%, which indicate the complete mineralization of BPA. GC-MS analysis was carried to find out the possible intermediates formed and reaction pathway.