Tag: DSB

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…

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Aedes aegypti Argonaute 2 controls arbovirus infection and host mortality

Generation and characterization of Ago2 knockout mutants To demonstrate the essential function of Ago2 in the Ae. aegypti siRNA pathway, we used CRISPR/Cas9 to knock out Ago2 and then investigated its role in defending against arbovirus infection (Fig. 1a). Ae. aegypti Ago2 (AeAgo2) has four exons and four predicated functional domains,…

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Screening non-conventional yeasts for acid tolerance and engineering Pichia occidentalis for production of muconic acid

Screening non-conventional yeast strains for organic acid tolerance To build a library of non-conventional yeasts for screening prospective acid tolerant hosts, we surveyed public culture repositories for non-Saccharomyces strains, selecting strains with reported acid tolerance where available. In total, 153 strains from 83 distinct species were obtained, of which 124…

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Luecken Cite-seq human bone marrow 2021 preprocessing

Dataset published by Luecken et al. 2021 which contains data from human bone marrow measured through joint profiling of single-nucleus RNA and Antibody-Derived Tags (ADTs) using the 10X 3′ Single-Cell Gene Expression kit with Feature Barcoding in combination with the BioLegend TotalSeq B Universal Human Panel v1.0.  File Description cite_quality_control.h5mu:…

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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….

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Identify the underlying mechanism associated with the initiation of focal amplification in breast cancer

In breast cancer, the focal amplification of oncogenes plays a critical role in oncogenesis. A recent study published in Nature used whole-genome sequencing (WGS), RNA sequencing, and epigenomic data to identify the underlying mechanism associated with the initiation of focal amplification in breast cancer. Study: ERα-associated translocations underlie oncogene amplifications in breast…

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Metagenomi Swiftly Variegates Gene-Editing Palatte

Despite the rapid development of genetic medicines, Simon Harnest, chief investment officer and SVP strategy at Metagenomi, said that attending the annual ASGCT meeting is a good way to keep tabs on the industry. “There are so many specialized groups in gene editing, some that focus on base editing and…

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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…

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Researchers discover a way to improve nonviral gene editing as well as a new type of DNA repair

Modification of HDRTs with interstrand crosslinks increases HR during gene editing. (a) Top panel: Cas9 RNPs introduce a double strand DNA break (DSB) at a targeted region in the genome, which can be repaired by error prone end joining (EJ) processes that rejoin the ends of the break, or homology-directed…

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Advances in CRISPR/Cas gene therapy for inborn errors of immunity. | Front Immunol;14: 1111777, 2023.

ABSTRACT Inborn errors of immunity (IEIs) are a group of inherited disorders caused by mutations in the protein–coding genes involved in innate and/or adaptive immunity. Hematopoietic stem cell transplantation (HSCT) is a mainstay definitive therapy for many severe IEIs. However, the lack of HLA-matched donors increases the risk of developing…

Continue Reading Advances in CRISPR/Cas gene therapy for inborn errors of immunity. | Front Immunol;14: 1111777, 2023.

Application of CRISPR/Cas9-mediated gene editing for abiotic stress management in crop plants

1 Introduction Abiotic stresses such as drought, heat, cold, salt, pesticides, metals and metalloids deteriorate agro-ecological conditions and hence, negatively impact upon agricultural production. The abiotic stress impairs with regular growth and development of plant plants, thus limiting their yield and quality of produce (Boyer, 1982; Pandey et al., 2017). Plants…

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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…

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Optimization of Cas9 activity through the addition of cytosine extensions to single-guide RNAs

Cell culture We cultured mESCs in t2iL medium containing Dulbecco’s modified eagle medium (DMEM, Nacalai Tesque), 2 mM Glutamax (Nacalai Tesque), 1× non-essential amino acids (Nacalai Tesque), 1 mM sodium pyruvate (Nacalai Tesque), 100 U ml−1 penicillin, 100 μg ml−1 streptomycin (P/S) (Nacalai Tesque), 0.1 mM 2-mercaptoethanol (Sigma) and 15% fetal bovine serum (FBS) (Gibco), supplemented with…

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Cutting With CRISPR: Assessing Safety as Technology Moves Into the Clinic

CRISPR/Cas is a genome-editing technology, which was recently recognized by a Nobel Prize in Chemistry in 2020 awarded to Emmanuelle Charpentier and Jennifer Doudna. CRISPR/Cas is currently associated with exciting medical applications; however, research into CRISPR/Cas began on its role as a bacterial immune defense system, by cleaving viral DNA….

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JCI – POLQ inhibition elicits an immune response in homologous recombination-deficient pancreatic adenocarcinoma via cGAS/STING signaling

ResearchIn-Press PreviewCell biology Open Access | 10.1172/JCI165934 Grace Oh,1 Annie Wang,2 Lidong Wang,2 Jiufeng Li,2 Gregor Werba,1 Daniel Weissinger,1 Ende Zhao,2 Surajit Dhara,2 Rosmel E. Hernandez,2 Amanda Ackermann,2 Sarina Porcella,3 Despoina Kalfakakou,2 Igor Dolgalev,4 Emily A. Kawaler,2 Talia Golan,5 Theodore H. Welling,1 Agnel Sfeir,3 and Diane M. Simeone1 1Department of…

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How cancer cells repair DNA damage from radiotherapy

A team of scientists led by Kei-ichi Takata from the Center for Genomic Integrity (CGI) within the Institute for Basic Science (IBS) in South Korea, has discovered a new type of DNA repair mechanism that cancer cells use to recover from next-generation cancer radiation therapy. Ionizing radiation (IR) therapy is…

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Chromosomal instability as central hallmark of Breast Cancer

Introduction In recent years, CIN has gained great importance due to its implications for both, the diagnosis and prognosis of cancer. Recent studies have suggested that both CIN and clonal heterogeneity, influence cancer progression, aggressiveness, prognosis, and response to therapy.1–4 The above because both, CIN and clonal heterogeneity, lead to…

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IJMS | Free Full-Text | Transcriptomic Analysis of CRISPR/Cas9-Mediated PARP1-Knockout Cells under the Influence of Topotecan and TDP1 Inhibitor

1. Introduction The synthesis of poly(ADP-ribose) (PAR) is an immediate response of cells to DNA damage catalyzed by poly(ADP-ribose) polymerases, which transfer ADP-ribose units from NAD+ onto target molecules [1]. PAR is a linear and branched polymer up to 200 units long that is covalently attached to the target proteins,…

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News: Cas12a chRDNA – A Novel Approach to Gene-Editing Therapy. Interview with Caribou Biosciences’ CSO Steve Kanner, Ph.D.

Steve Kanner, Ph.D. has been the Chief Scientific Officer of Caribou Biosciences since 2017, and is responsible for the company’s therapeutic discovery, research, and development activities. Steve received his undergraduate degree in Genetics from the University of California, Berkeley, and his Ph.D. in Immunology and Microbiology from the University of…

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Genome editing techniques based on bacterial-artificial-chromosome in herpesvirus research

In a recent study published in the Microorganisms journal, researchers in China reviewed the uses of bacterial-artificial-chromosome (BAC)-based genome editing techniques in herpesvirus research. Review: Bacterial-Artificial-Chromosome-Based Genome Editing Methods and the Applications in Herpesvirus Research. Image Credit: Panuwach / Shutterstock Herpesviruses are significant human and animal pathogens. Exploring the role of specific…

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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…

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Hypersaline Lake Urmia: a potential hotspot for microbial genomic variation

Physico-chemical features of Lake Urmia Sampling was performed during the period of lowest rainfall and input volume in the year when the lake water reached the highest salt concentration (locations shown in Fig. 1, Supplementary Table S1). The measured ionic composition of the collected brine showed the typical composition of halite-dominated…

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Clonal dynamics underlying the skewed CD4/CD8 ratio of mouse thymocytes revealed by TCR-independent barcoding

Implementation of a high-resolution barcoding system In order to determine the clonal relationships of developing thymocytes, we used an endogenous barcoding system (Fig. 1a) that consists of three components19. (i) A construct for the ubiquitous expression of the Hprt gene-specific sgRNA (hU6:sgRNAHprt)19; (ii) A conditional Cas9 expression construct (Rosa26:LSL-Cas9-YFP) inserted into…

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Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3

In vitro reconstitution of Escherichia coli CRISPR-Cas3 interference E. coli CRISPR-Cas3 is generally well-characterized type I CRISPR complexes in vitro and in vivo32,33,37,38. However, recombinant EcoCas3 protein is difficult to purify because of poor solubility and propensity to aggregate at 37 °C25,26,30,39. Co-expression of HtpG chaperon40 and/or low temperature growth at…

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Genome-wide investigation of multiplexed CRISPR-Cas12a-mediated editing in rice

Abstract We previously reported highly specific genome editing in rice by CRISPR-Cas9 and Cas12a with single DNA double strand break (DSB) (Tang et al., 2018). Two concurrent DSBs by CRISPR-Cas9 could generate defined deletions (Zhou et al., 2014), inversions (Schmidt et al., 2020), and translocations (Beying et al., 2020). Off-target…

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Frontiers | A Mutated Nme1Cas9 Is a Functional Alternative RNase to Both LwaCas13a and RfxCas13d in the Yeast S. cerevisiae

Introduction The clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) protein systems naturally exist in prokaryotes. They are RNA-mediated defense mechanisms to protect bacteria and archaea from invading nucleic acids (Barrangou et al., 2007). CRISPR–Cas systems are classified into two classes (1 and 2). Class 2 CRISPR–Cas require a single…

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CRISPR/Cas9 deletions induce adverse on-target genomic effects

Clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) have transformed genome engineering techniques. Numerous toolsets have been created to enable easy and efficient loss-of-function perturbations of functional genomic sites. Study: CRISPR/Cas9 deletions induce adverse on-target genomic effects leading to functional DNA in human cells. Image Credit: elenabsl/Shutterstock The CRISPR/Cas9 system’s elements…

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Assistant Professor of bioinformatics and metagenomics at Novo Nordisk Foundation Center for Protein Research

Job title: Assistant Professor of bioinformatics and metagenomics at Novo Nordisk Foundation Center for Protein Research Company: Workscout Job description Job beskrivelse We are looking for a highly motivated and dynamic Assistant Professor for a 4-year position to commence on the 1st of April 2022 or soon hereafter. The position…

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Assistant Professor Job – Bioinformatics and Metagenomics, UCPH, Denmark, Jan 2022

The University of Copenhagen invites applications for an Assistant Professor position will be in the Human Proteome Variation group at The Novo Nordisk Foundation Center for Protein Research, Denmark – Jan 2022 Qualification Details Six overall criteria apply for Assistant Professor appointments at the University of Copenhagen. The six criteria…

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Sigma-Aldrich and Broad Propose Preliminary Motions in Recent CRISPR Interference No. 106,133 | McDonnell Boehnen Hulbert & Berghoff LLP

The parties in Interference No. 106,133, namely Senior Party Sigma-Aldrich and Junior Party the Broad Institute, Harvard University, and MIT (collectively, “Broad”), filed their respective lists of proposed preliminary motions four days prior to their August 3rd teleconference with the Board to present their arguments for the Board to grant…

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Postdoc in bioinformatics and metagenomics at Novo Nordisk Foundation Center for Protein Research – University of Copenhagen – job portal

Job Portal Postdoc in bioinformatics and metagenomics at Novo Nordisk Foundation Center for Protein Research We are looking for a highly motivated and dynamic researcher for a 2 year position, to commence on 1 January 2022 or soon hereafter. The position will be in the Human Proteome Variation group at The Novo Nordisk…

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Detecting NUMTS (nuclear mitochondrial sequences) in the whole genome sequenced data

Detecting NUMTS (nuclear mitochondrial sequences) in the whole genome sequenced data 0 Hi All, I want to detect NUMTS (nuclear mitochondrial sequences) that have migrated from the mitochondrial to the nuclear genome using the whole genome sequence data. What could be the best Bioinformatic approach ?? Their presence, extent and…

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