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Functional genomic screening in Komagataella phaffii enabled by high-activity CRISPR-Cas9 library
Abstract CRISPR-based high-throughput genome-wide loss-of function screens are a valuable approach to functional genetics and strain engineering. The yeast Komagataella phaffii is a host of particular interest in the biopharmaceutical industry and as a metabolic engineering host for proteins and metabolites. Here, we design and validate a highly active 6-fold…
Gadolinium Oxide Nanoparticles reinforce immune response
Boyi Yu,1– 4 Xuanyi Lu,5 Xianglong Feng,1– 4 Ting Zhao,1– 4 Jiaxin Li,1– 4 Yudie Lu,5 Fei Ye,1– 4 Xiongxiong Liu,1– 4 Xiaogang Zheng,1– 4 Zheyu Shen,5 Xiaodong Jin,1– 4 Weiqiang Chen,1– 4 Qiang Li1– 4 1Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of…
Shaping the Future of Targeted Drug Development
The need for targeted drugsCRISPR/Cas9 in drug discoveryPrecision medicine and personalized therapiesFuture prospects and conclusionsReferences Further reading Clustered regular interspaced short palindromic repeat/CRISPR-associated 9 (CRISPR/Cas9) is a gene-editing technology that has revolutionized biomedical research since its original publication in 2012. The two primary components involved in CRISPR/Cas9 include a guide ribonucleic…
CRISPR Gene Editing: Cas9 and Beyond
Scientists use the CRISPR-Cas9 system to target a DNA sequence of interest near a protospacer-adjacent motif (PAM). The PAM initiates Cas9-DNA binding, a guide RNA (yellow) invades the double helix (blue) and hybridizes with the target DNA, and Cas9 (red) breaks the unwound double-stranded target DNA. iStock Meletios Verras Stay…
CRISPR-Cas9 Gene Editing Is On The Cusp Of Something Big
Natali_Mis Gene editing, also known as genome editing, is a method where the DNA of an organism is modified using biotechnological techniques. It allows scientists to add, remove, or alter genetic material at particular locations in the genome. This 2-part series will cover the basics of CRISPR-Cas9 (see below) in…
Decline of DNA damage response along with myogenic differentiation
Introduction Proper functioning of all living organisms depends on the faithful maintenance and transmission of genomic information stored in the molecule of DNA. However, DNA integrity is continuously challenged by a variety of endogenous and exogenous agents causing DNA lesions which have a critical impact on cellular activities and homeostasis….
What Is CRISPR Technology | CitizenSide
History of CRISPR Technology The history of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology traces back to the early 1990s when scientists first noticed repetitive DNA sequences in the genomes of certain bacteria. However, it wasn’t until 2005 that the true potential of CRISPR was realized. It was in…
Integration of xeno-free single-cell cloning in CRISPR-mediated DNA editing of human iPSCs improves homogeneity and methodological efficiency of cellular disease modeling
. 2023 Nov 8:S2213-6711(23)00415-0. doi: 10.1016/j.stemcr.2023.10.013. Online ahead of print. Affiliations Expand Affiliations 1 Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia. 2 Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine…
IJMS | Free Full-Text | CRISPR/Cas9-Mediated Genome Editing in Cancer Therapy
1. Introduction Recently, the morbidity and mortality rates of cancer have been increasing rapidly, posing a significant threat to human health. Cancer, a refractory and multifaceted disease, fundamentally originates from a cumulative series of mutations in the cellular genome and epigenome. These mutations activate oncogenes and deactivate tumor suppressors, leading…
IJMS | Free Full-Text | CRISPR/Cas9 Directed Reprogramming of iPSC for Accelerated Motor Neuron Differentiation Leads to Dysregulation of Neuronal Fate Patterning and Function
1. Introduction As the world population ages, neurodegenerative diseases are increasing. The outcome of these diagnoses varies but can lead to fatality 50% of the time within 15–20 months [1]. Treatments for neurodegeneration, in particular motor neuron (MN) diseases, are restricted due to the limitations of motor neuron repair and…
Summary of CRISPR-Cas9 off-target Detection Methods
Genome editing technology stands at the forefront of current life science research. However, for its successful translation into clinical applications, the accurate detection of off-target effects is indispensable. Assessing and mitigating off-target effects correctly is a pressing concern. The issue of off-target effects in CRISPR-Cas9 gene editing technology has been…
The Hidden Mechanisms Behind Rapid Tumor Evolution: AR Amplification on Extrachromosomal DNA I Prostate Cancer
Read the Full Video Transcript Andrea Miyahira: Hi everyone, I’m Andrea Miyahira at the Prostate Cancer Foundation. Presenting today is Dr. Scott Dehm, a professor at the University of Minnesota on his recent paper, “Co-evolution of AR gene copy number and structural complexity in endocrine therapy resistant prostate cancer,” published…
CRISPR/Cas9 bioluminescence-based assay for monitoring CFTR trafficking to the plasma membrane
Introduction Cystic fibrosis (CF) is a lethal, autosomal recessive disorder caused by mutations in the CFTR gene that results in aberrant transport of chloride, bicarbonate, and sodium ions (Kerem et al, 1989; Riordan et al, 1989; Rommens et al, 1989; Tabcharani et al, 1991; Poulsen et al, 1994; Stutts et…
A Discussion with Dr. Wenning Qin
In this interview, we delve deep into the pioneering world of xenotransplantation and the evolving landscape of gene editing, with Dr. Wenning Qin, SVP, Innovation & Process Development at eGenesis. Drawing from her vast experience, Dr. Qin shares insights into the challenges, opportunities, and future of xenotransplantation. Please introduce yourself…
What is the main advantage of induced pluripotent stem cells iPSCs in
a) Gene therapy targets somatic cells, while knockout models target germline cells. b) Gene therapy targets germline cells, while knockout models target somatic cells. c) Gene therapy uses NHEJ, while knockout models use HDR. d) Gene therapy targets embryos, while knockout models target adult organisms. **Yamanaka Factors and Regenerative Medicine:**…
Explained: What is CRISPR gene editing and how does it work?
CRISPR-Cas9, often simply referred to as CRISPR, is a revolutionary gene-editing tool that has transformed the field of genetics. In this explainer, we’ll unravel the mysteries of CRISPR gene editing and explore how it works, its applications, and its ethical considerations.The CRISPR RevolutionBefore we dive into the mechanics of CRISPR,…
Precise genome editing human stem cells for functional interrogation of genetic variation
Abstract Human induced pluripotent stem cells (iPSCs) provide great potential as a tool for basic biological discovery, disease modeling, and ultimately for cell based regenerative medicine but the full realization of these stem cells requires an ability to precisely edit their genome in an efficient way. The relative efficiencies of…
IJMS | Free Full-Text | CRISPR-Cas9 Direct Fusions for Improved Genome Editing via Enhanced Homologous Recombination
Over the past decade, CRISPR-Cas9 has found widespread application in loss-of-function mutations, but precise genetic engineering for gene correction or gene replacement therapies has lagged behind. In vivo correction using CRISPR-Cas9 to replace genetic mutations by HR is highly challenging, and very few studies have managed to achieve this [31,32]….
Targeting MTHFD1 and MTHFD2 as cancer treatment
Abstract: One-carbon (1C) metabolism provides building blocks for nucleotide synthesis and therefore plays a central role in DNA replication and repair. To sustain rapid proliferation, cancer cells often upregulate their 1C metabolism, including the enzymes MTHFD1 and MTHFD2, as a part of their metabolic rewiring. Previously, MTHFD2 in particular has…
Orthogonal Validation: A Means To Strengthen Gene Editing and Gene Modulation Research
From RNA interference (RNAi) to CRISPR, there are several methods that researchers can use to manipulate gene function, each with its own strengths and weaknesses. Orthogonal validation – the synergistic use of different methods – makes genetic perturbation studies more robust. Utilizing complementary methods, including RNAi and CRISPR-knockout, -interference and…
Gene Editing Tools Based on CRISPR/Cas System and Their Improvement Strategies
Gene Editing Tools Based on CRISPR/Cas System and Their Improvement Strategies XIN Yuan1,TIAN Kai-ren3,QIAO Jian-jun1,2,3,CAIYIN Qing-ge-le1,2,**() 1 School of…
A DNA assembly kit to unlock the CRISPR-Cas9 potential for metabolic engineering
Modular toolkit structure – The toolkit consists of seven modules for quick and easy assembly of integrative constructs and Cas9-helper plasmids. Lvl0 Module: single parts in entry vectors. Exp Module: assembly of overexpression constructs. Pro Module: assembly and screening of new promoters. Del Module: assembly of disruption constructs. Int Module:…
A DNA assembly toolkit to unlock the CRISPR/Cas9 potential for metabolic engineering
Nielsen, J., Larsson, C., van Maris, A. & Pronk, J. Metabolic engineering of yeast for production of fuels and chemicals. Curr. Opin. Biotechnol. 24, 398–404 (2013). Article CAS PubMed Google Scholar DiCarlo, J. E. et al. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 41, 4336–4343 (2013)….
Research raises hopes for new treatment of fusion-driven cancer
Fusion-gene disruption strategy. A Dual intron-targeting CRISPR-Cas9-mediated disruption of RUNX1-RUNX1T1. sgRNAs targeting intron 4 of RUNX1 (orange) and intron 1a of RUNX1T1 (green) are indicated. Cas9 cleavage at target sites within intron 4 of RUNX1 and intron 1a of RUNX1T1 leads to a major deletion of exon 5 in RUNX1…
Scientists Promote Novel Globin Genetic Therapy for Sickle Cell Disease
By Kevin Davies, PhD Mandy Boontanrart, PhD Mandy Boontanrart, PhD, a postdoc at ETH Zurich in Switzerland, has a particularly personal motivation for her research on a novel genetic therapy for sickle cell disease (SCD). She is a carrier of a mutation for another hemoglobinopathy, alpha thalassemia. She initially received…
Next-Generation Sequencing in CRISPR Gene Editing Assessment and Quality Control
The advent of CRISPR-Cas9 gene editing technology has undeniably revolutionized the landscape of genetic research and therapeutic applications. Its ability to precisely modify specific regions of the genome has opened unprecedented opportunities for treating genetic disorders and driving advancements in biotechnology. However, harnessing the full potential of this revolutionary tool…
Can genome editing transform ocular disease treatment?
In a recent review published in Experimental & Molecular Medicine, researchers reviewed existing data on the discovery and development of gene-editing technologies and their applications in managing ocular diseases. Study: Genome editing in the treatment of ocular diseases. Image Credit: GarnaZarina/Shutterstock.com Background Gene therapy advances offer a new therapeutic approach for various…
SOHM Inc. Signs LOI to Acquire Stem Cell Disruptive Technology and Patents
PRESS RELEASE Published August 1, 2023 CHINO HILLS, CA/ ACCESSWIRE/ / August 1, 2023 / SOHM, Inc. (OTC PINK:SHMN), a generic pharmaceutical, nutraceutical and cosmeceutical company that manufactures and markets generic drugs covering numerous treatment categories, announces today that the company has signed a letter of intent to acquire stem…
The complementarity of DDR, nucleic acids and anti-tumour immunity
Decout, A., Katz, J. D., Venkatraman, S. & Ablasser, A. The cGAS–STING pathway as a therapeutic target in inflammatory diseases. Nat. Rev. Immunol. 21, 548–569 (2021). Article CAS PubMed PubMed Central Google Scholar Martincorena, I. & Campbell, P. J. Somatic mutation in cancer and normal cells. Science 349, 1483–1489 (2015)….
Long-read sequence analysis of MMEJ-mediated CRISPR genome editing reveals complex on-target vector insertions that may escape standard PCR-based quality control
Overview of the targeting strategy Figure 1A presents an overview of the MMEJ-mediated genome-editing system PITCh12,13. The full-length sequence of the targeting vector is shown in Supplementary Fig. 1. The PITCh method can be classified into three types according to the number of cutting sites in the genome and the targeting vector….
CRISPR-Cas Gene Editing Teaching Resources | Bio-Rad / Free Group Study Rooms with Timer & Music
One of the most exciting recent developments in genetic engineering is CRISPR-Cas9 (CRISPR). CRISPR derives its name from “clustered regularly interspaced short palindromic repeats,” genomic sequences that microbiological used to defending themselves vs viral attacks. Along with CRISPR associated (Cas) bio, bacteria use the sequences toward recognize and disarm future…
Epistatic interactions between the high pathogenicity island and other iron uptake systems shape Escherichia coli extra-intestinal virulence
Begier, E. et al. Epidemiology of invasive Escherichia coli infection and antibiotic resistance status among patients treated in US hospitals: 2009-2016. Clin. Infect. Dis. Publ. Infect. Dis. Soc. Am. 73, 565–574 (2021). Article CAS Google Scholar Bélanger, L. et al. Escherichia coli from animal reservoirs as a potential source of…
Design of bacteriophage T4-based artificial viral vectors for human genome remodeling
Assembly of T4 artificial viral vectors T4-AVVs were assembled by sequential incorporation of purified biomaterials to generate a virus structural mimic (Fig. 2a and Supplementary Movie 1). Starting with an empty capsid shell purified from E. coli infected by the neck-minus and tail-minus T4 phage mutant (10-amber.13-amber.HocΔ.SocΔ T4) (Supplementary Fig. 1a), a pentameric…
ssDNA is not superior to dsDNA as long HDR donors for CRISPR-mediated endogenous gene tagging in human diploid RPE1 and HCT116 cells | BMC Genomics
An optimized CRISPR knock-in method using long dsDNA donors for efficient tagging with fluorescent proteins in human diploid cells. Given the widespread use of CRISPR-mediated generation of knock-in cell lines, it is informative to compare the performance of long dsDNA and ssDNA donors in a simple and practical knock-in method….
The following figure shows a part of a plasmid vector
Transcribed image text: The following figure shows a part of a plasmid vector pCFD3 for the expression of a sgRNA. The orange sequences are part of a strong promoter (transcription from this promoter starts at the G in bold-which must be present-and goes from left to right). The purple sequences…
ncRNA | Free Full-Text | Inverse Impact of Cancer Drugs on Circular and Linear RNAs in Breast Cancer Cell Lines
Received: 19 January 2023 / Revised: 2 May 2023 / Accepted: 16 May 2023 / Published: 19 May 2023 Round 1 Reviewer 1 Report Terrazan and coworkers presented the manuscript entitled “ Inverse impact of cancer drugs on circular and linear RNAs in 2 breast cancer cell lines ”. The…
NeuBase Announces Formation of Gene Editing Advisory Board
PITTSBURGH, May 16, 2023 (GLOBE NEWSWIRE) — NeuBase Therapeutics, Inc. (Nasdaq: NBSE) (“NeuBase” or the “Company”), a biotechnology company developing Stealth Editors™ to perform in vivo gene editing without triggering the immune system, today announced the formation of a gene editing advisory board comprised of distinguished leaders of the scientific community…
Non-Viral Gene Editing Enhanced by Interstrand Cross Links
– Advertisement – Researchers from the University of California, Santa Barbara have developed a new CRISPR/Cas9 genome-editing method that increases efficiency without the use of viral material. The CRISPR-Cas9 method uses a defence mechanism first discovered in archaea to protect bacteria against viral attacks. The bacteria cuts a fragment of…
Enhancement of Non-Viral Gene Editing Through Interstrand Cross Links
– Advertisement – Researchers at the University of California (UC) Santa Barbara have developed a method that improves CRISPR/Cas9 editing efficiency without using viral material. The CRISPR-Cas9 method uses a defence technique first discovered in archaea and later in bacteria to protect against viral invaders. The bacteria “cut” a fragment…
Interstrand Cross Links Improve Non-Viral Gene Editing
Register for free to listen to this article Thank you. Listen to this article using the player above. ✖ Want to listen to this article for FREE? Complete the form below to unlock access to ALL audio articles. University of California (UC) Santa Barbara researchers have added…
Stable expression of large transgenes via the knock-in of an integrase-deficient lentivirus
CLIP enables high-efficiency knock-in into an essential locus To create CLIP, we leverage integrase-deficient lentiviruses (IDLV) to deliver an HDR donor template as a viral RNA genome to cells25,26. IDLV consists of lentiviral components but with a D64V mutation in the integrase, maintaining this enzyme’s ability to package and nuclear…
Topologically associating domain boundaries are required for normal genome function
ENCODE ChIP-seq data analysis and prioritization of TAD boundary deletion loci Previously published chromosome conformation capture data was used for combined analyses and selection of TAD boundary deletion loci in this study, wherein TAD boundary calls were based on the maximum enrichment of CTCF at the TAD borders and their…
Nanoparticle-based combination therapy for ovarian cancer
Introduction Ovarian cancer is one of the most common gynecologic malignancies with high morbidity.1 Due to its relatively asymptomatic nature, about 70% of patients are diagnosed at an advanced stage and have poor prognosis, leading to high mortality rates.2,3 The clinical treatment of ovarian cancer mainly relies on chemotherapy after…
The DREAM complex functions as conserved master regulator of somatic DNA-repair capacities
C. elegans strains All strains were cultured under standard conditions78 and were always incubated at 20 °C during the experiments. The strains used were N2 (Bristol; WT): DREAM: MT8839 lin-52(n771) III, MT10430 lin-35(n745) I, MT15107 lin-53(n3368) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III), MT8879 dpl-1(n2994) II, MT11147 dpl-1(n3643) II, JJ1549 efl-1(se1) V, BJS634…
How to overcome the biggest challenges in cell line development
The advancement of cell line engineering and microfluidic technologies offers a range of benefits in terms of reducing the duration of cell line development (CLD). Optimizing CLD processes can also present new difficulties and uncertainties. Four of the most crucial challenges in this regard are: 1) The potential for selection…
A Comprehensive Guide to CRISPR Screening and Sequencing: Methods, Applications, and Challenges
In competition with bacteriophages, bacteria and archaea have evolved unique ways of defending, which include the CRISPR/Cas systems and the immune systems of bacteria and archaea, which resist the invasion of foreign DNA or RNA and recognize the foreign invaders and cleave them for immune defense. CRISPR/Cas systems are…
IJMS | Free Full-Text | High-Efficiency CRISPR/Cas9-Mediated Correction of a Homozygous Mutation in Achromatopsia
1. Introduction Achromatopsia (ACHM) is an inherited retinal dystrophy (IRD) affecting approximately 1 in every 30,000 individuals [1,2]. It is an autosomal-recessive disorder associated with a loss of cone photoreceptor function [1,2,3,4]. ACHM usually shows an early onset presenting pendular nystagmus, poor visual acuity, lack of color vision, and photophobia…
The CRISPR-Cas12a Platform for Accurate Genome Editing, Gene Disruption, and Efficient Transgene Integration in Human Immune Cells
journal contribution posted on 2023-02-08, 00:43 authored by Marina Mohr, Nkerorema Damas, Johanne Gudmand-Høyer, Katrine Zeeberg, Dominika Jedrzejczyk, Arsenios Vlassis, Martí Morera-Gómez, Sara Pereira-Schoning, Urška Puš, Anna Oliver-Almirall, Tanja Lyholm Jensen, Roland Baumgartner, Brian Tate Weinert, Ryan T. Gill, Tanya Warnecke CRISPR-Cas12a nucleases have expanded the toolbox for targeted genome…
C698R mutation in Lrsam1 gene impairs nerve regeneration in a CMT2P mouse model
Animal generation The Lrsam1C698R knock-in mice were generated on a C57Bl/6J background using the CRISPR/Cas9 technique. Briefly, single-cell zygotes from C57BL/6J mice were microinjected with mRNA encoding Cas9 and a guide sequence (5′-ACAGCAGCAGACGTGGCCAC-3′ at 20 ng/µl) to target the exon 26 of Lrsam1. A single stranded DNA oligo carrying the C698R mutation…
CRISPR Gene Detection and Diagnostic Industry 2022 Market Size, Share and Growth, Global Segments Analysis and Dynamic Research Report 2029
The Wide Ranging CRISPR Gene Detection and Diagnostic Business Report encompasses a thorough study of current situation of the global market along with several market dynamics. The market research report is a demonstrated source of information which offers a telescopic view of the current market trends, size, share, growth, demand,…
Sigma-Aldrich Files Substantive Preliminary Motion No. 1 to Deny Broad Priority Benefit to Its Earliest-filed Provisional Application | McDonnell Boehnen Hulbert & Berghoff LLP
On December 3rd, Senior Party Sigma-Aldrich filed its Substantive Preliminary Motion No. 1 in Interference No. 106,133 (which names the Broad Institute, Harvard University, and MIT (collectively, Broad) as Junior Party), asking the Patent Trial and Appeal Board to deny Broad benefit of its U.S. Provisional Application No. 61/736,527, filed…
Increased BUB1B/BUBR1 expression contributes to aberrant DNA repair activity leading to resistance to DNA-damaging agents
This article was originally published here Oncogene. 2021 Sep 20. doi: 10.1038/s41388-021-02021-y. Online ahead of print. ABSTRACT There has been accumulating evidence for the clinical benefit of chemoradiation therapy (CRT), whereas mechanisms in CRT-recurrent clones derived from the primary tumor are still elusive. Herein, we identified an aberrant BUB1B/BUBR1 expression…
2020 Heritable Human Genome Editing – Genômica
editing methodologies. It is possible that continuing research may yield new methodologies that rapidly supersede the safety and efficacy of current editing approaches. Non-Heritable Genome Editing: The Use of Genome Editing in Somatic Cells One potential alternative to HHGE for the treatment of genetic dis- eases is somatic genome…
New Results from BabySeq, Pharmacogenomic Updates, New Products
September 1, 2021 | Harvard-Israel and Sema4-Avera launch precision medicine partnerships, Rice announces new Genetic Design and Engineering Center, Foundation Medicine partners with Epic, and Amgen and USC provide cryo-TEMs. Plus new products from BioIVT, BD. Pluto Biosciences has launched its cloud-based, collaborative life sciences platform that leverages technology…
Validation of gene editing efficiency with CRISPR-Cas9 system directly in rat zygotes using electroporation mediated delivery and embryo culture
doi: 10.1016/j.mex.2021.101419. eCollection 2021. Affiliations Expand Affiliations 1 Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA. 2 Cystic Fibrosis Research Center, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA. Free PMC article Item in Clipboard Anil K Challa et al….
CRISPR: Guide to gRNA design
Introduction to CRISPR in SnapGene Genome editing technology has been evolving for many years. The Holy Grail of genome engineering has always been to introduce a specific genetic change that affects only the genomic target and leaves no undesired changes in the DNA. The discovery and application of the bacterial…
CVC Files Opposition to ToolGen’s Substantive Preliminary Motion No. 2 | McDonnell Boehnen Hulbert & Berghoff LLP
In June, Senior Party ToolGen filed its Substantive Preliminary Motion No. 2 to deny Junior Party the University of California, Berkeley; the University of Vienna; and Emmanuelle Charpentier (collectively, “CVC”) priority benefit to its U.S. Provisional Application No. 61/757,640, filed January 28, 2013 (“Provisional 3”), pursuant to 37 C.F.R. §§…