Tag: DSB

CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated protein) genome editing enables precise, targeted genetic modification of plants. To date, the genomes of several crops, including rice, tomato, corn, wheat, soybean, barley, potato, sorghum, apple, grapefruit, and orange, have been edited using CRISPR-Cas-based genome editing technology. The CRISPR system cuts not…

Introduction Homologous recombination (HR) is an evolutionarily conserved process that plays a pivotal role in genome stability, diversity, and plasticity. HR is indeed a key repair pathway able to faithfully repair DNA damages including double-strand breaks (DSBs) and DNA gaps by copying the error-free information from the template DNA normally…

CHEK2 expression increased in cancer tissues First, the expression levels of CHEK2 in different tumor types in the TIMER database were evaluated. All tumors except for chromophobe renal cell carcinoma (KICH) showed elevated levels of CHEK2 expression compared to normal cells (Fig. 1A). Similarly, CHEK2 protein expression was upregulated in all…

journal contribution posted on 2023-12-09, 04:41 authored by Mohammadreza M. Mehryar, Xin Shi, Jingwei Li, Qiang Wu Additional file 1: Fig. S1. DNA-fragment editing by Cas9 with dual sgRNAs. Fig. S2. HPRT1 and DCK reporter assay systems for Cas9-induced large resections. Fig. S3. Quantitative RT-PCR at two time points in HEC-1-B…

Cell culture The human endometrial carcinoma HEC-1-B cells were cultured in the modified Eagle’s medium (MEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a 5% (v/v) CO2 incubator. The human embryonic kidney HEK293T cells were cultured in the Dulbecco’s modified Eagle’s medium (DMEM) supplemented…

mitoARCUS localizes to the mitochondrial matrix To evaluate the ability of mitoARCUS to specifically cleave m.3243G mutant mtDNA, cell lines containing varying levels of the mutation were generated. All of these cell lines were isolated from the same parental m.3243A>G cybrid cell line. Levels of the m.3243G mutation of each…

Fig 1. Cleavage of the oligonucleotide or the plasmid substrates by Cas9/sgRNA in the presence of PARP1 and PARP2. Cas9/sgRNA (10 nM) was incubated with 32P-labelled dsDNA1*/2 or dsDNA1/2* (10 nM; A, B) or with pLK1 DNA (10 ng/μl; C, D) and the indicated amounts of NAD+, PARP1 (A, C)…

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…

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….

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…

Introduction The CRISPR-Cas system is a widely used genome engineering technology because of its simple programmability, versatile scalability, and targeting efficiency (Wang & Doudna, 2023). Although researchers are rapidly developing CRISPR-Cas9 tools, the biggest challenge remains to overcome undesired on- and off-targeting outcomes. Previous studies have reported unintended genomic alterations,…

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…

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…

BISO’s academic association, DSB (Data Science for Business), are hosting a “Beginner Python & RStudio Workshop” on November 9th at 17:00 in room C2-095. This event is aimed at assisting students in developing their programming skills and expanding their knowledge in Python and RStudio. Here’s what you can expect at…

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…

Reviewed by Lily Ramsey, LLMOct 26 2023 Precision genome editing technologies have transformed modern biology. Capabilities for programable DNA targeting have improved rapidly, largely due to the development of bacterial RNA-guided CRISPR-Cas systems, which allow precise cleavage of target DNA sequences. However, CRISPR-Cas9 systems generate a DNA double strand break…

Patient characteristics and tissue context The clinical interpretation of molecular alterations starts with evaluating relevant patient characteristics and the tissue context in which a genetic profile occurs. The former relates, in particular, to previous therapies, in addition to disease stage and clinical performance status. For example, prior targeted therapies warrant…

In a Perspective, Stephen Tang and Samuel Sternberg discuss retroelement-based gene editing as a safer alternative to CRISPR-Cas approaches. Precision genome editing technologies have transformed modern biology. Capabilities for programable DNA targeting have improved rapidly, largely due to the development of bacterial RNA-guided CRISPR-Cas systems, which allow precise cleavage of…

In a recent study published in the journal Nature, researchers identify the mechanisms through which double-stranded break (DSB)-induced compartment formation orchestrates the deoxyribonucleic acid (DNA) damage response (DDR). Study: Chromatin compartmentalization regulates the response to DNA damage. Image Credit: CI Photos / Shutterstock.com Background DNA DSBs are extremely hazardous lesions that could…

Cell culture and treatments DIvA (AsiSI-ER-U2OS)19, AID-DIvA (AID-AsiSI-ER-U2OS)23 and 53BP1-GFP DIvA20 cells were developed in U2OS (ATCC HTB-96) cells and were previously described. Authentication of the U2OS cell line was performed by the provider ATCC, which uses morphology and short tandem repeat profiling to confirm the identity of human cell…

3 year Fixed Term Contract This is an exciting post-doctoral opportunity to carry out collaborative research with one of the world’s leading research institutes and one of the world’s leading pharmaceutical companies as a member of the Crick-GSK Prosperity Partnership team. The collaboration is developing a Systems Chemical Biology platform…

doi: 10.1093/mutage/gead031. Online ahead of print. Affiliations Expand Affiliation 1 Department of Genetics and Cytology, Yerevan State University, 1 Alex Manoogian, 0025 Yerevan, Armenia. Item in Clipboard Tigran Harutyunyan. Mutagenesis. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1093/mutage/gead031. Online ahead of print. Affiliation 1 Department of Genetics…

doi: 10.1038/s41421-023-00590-8. Affiliations Expand Affiliations 1 Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China. 2 School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China. 3 Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China. 4 Westlake Disease Modeling Lab, Westlake Laboratory of Life Sciences…

Introduction Cancer is well characterized by genomic instability resulting in structural alterations that build up with tumor progression.1,2 A subpopulation of undifferentiated cancer cells, known as cancer stem cells (CSCs) are found within the tumor bulk. These cells are responsible for cancer initiation, recurrence and show therapeutic resistance and these…

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]….

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…

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,…

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…

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:…

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….

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…

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…

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…

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…

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…

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…

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…

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…

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….

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…

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…

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…

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,…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…