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Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency

Understanding the impact of guide RNA (gRNA) and genomic locus on CRISPR-Cas9 activity is crucial to design effective gene editing assays. However, it is challenging to profile Cas9 activity in the endogenous cellular environment. Here we leverage our TRIP technology to integrate ~ 1k barcoded reporter genes in the genomes of mouse embryonic stem cells. We target the integrated...

Synthesis and characterization of titania nanotubes by anodizing of titanium in fluoride containing electrolytes

Titania nanotubular structure was prepared by anodizing titanium metal in the fluoride containing electrolytes and studied for hydrogen reduction using photo electrochemical cell. Potentiodynamic scan was performed before actual anodizing to optimize the anodizing conditions. The morphology of the TiO2 nanotubes was investigated by SEM and the presence of TiO2 nanotubes was...

High-throughput assessment of context-dependent effects of chromatin proteins

Background Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest. The assay combines a previously reported multiplexing strategy based on barcoded randomly integrated reporters with Gal4-mediated tethering. We applied the assay...

NitroSynapsin therapy for a mouse MEF2C haploinsufficiency model of human autism

Disease Center, Scintillon Institute, San Diego, CA, 92121, USAShichun Tu, Mohd Waseem Akhtar, James Parker, Kevin Lopez, Abdullah Sultan, Scott R. McKercher, Rajesh Ambasudhan, Stuart A. Lipton & Nobuki ... NakanishiNeuroscience and Aging Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USAShichun Tu, Mohd Waseem Akhtar, Rosa Maria Escorihuela, Alejandro Amador-Arjona, James Parker

Redox Regulation of Protein Function via Cysteine S-Nitrosylation and Its Relevance to Neurodegenerative Diseases

2012 Academic Editor: Pier Giorgio Mastroberardino Copyright © 2012 Mohd Waseem Akhtar et al. This is an open access article distributed under the Creative Commons Attribution License, which permits

TBP2 is a substitute for TBP in Xenopus oocyte transcription

Background TATA-box-binding protein 2 (TBP2/TRF3) is a vertebrate-specific paralog of TBP that shares with TBP a highly conserved carboxy-terminal domain and the ability to bind the TATA box. TBP2 is highly expressed in oocytes whereas TBP is more abundant in embryos. Results We find that TBP2 is proteolytically degraded upon meiotic maturation; after germinal vesicle breakdown...

Role of multidetector computed tomography (MDCT) in patients with ovarian masses

Role of multidetector computed tomography (MDCT) in patients with ovarian masses Fatima Mubarak, Muhammad Shahbaz Alam, Waseem Akhtar, Saima Hafeez, Noureen NizamuddinRadiology Department, Aga Khan ... . Conclusion: MDCT imaging offers a safe, accurate and noninvasive modality to differentiate between benign and malignant ovarian masses. Fatima Mubarak; Muhammad shahbaz Alam; Waseem Akhtar saima Hafeez n

Chromatin Landscapes of Retroviral and Transposon Integration Profiles

The ability of retroviruses and transposons to insert their genetic material into host DNA makes them widely used tools in molecular biology, cancer research and gene therapy. However, these systems have biases that may strongly affect research outcomes. To address this issue, we generated very large datasets consisting of to unselected integrations in the mouse genome for the...

Diagnosis of hepatoma using grayscale and Doppler ultrasound in patients with chronic liver disease

Diagnosis of hepatoma using grayscale and Doppler ultrasound in patients with chronic liver disease Wasim A Memon, Zishan Haider, Mirza Amanullah Beg, Muhammad Idris, Tanveer-ul-Haq, Waseem Akhtar

In Vivo Analysis of MEF2 Transcription Factors in Synapse Regulation and Neuronal Survival

MEF2 (A–D) transcription factors govern development, differentiation and maintenance of various cell types including neurons. The role of MEF2 isoforms in the brain has been studied using in vitro manipulations with only MEF2C examined in vivo. In order to understand specific as well as redundant roles of the MEF2 isoforms, we generated brain-specific deletion of MEF2A and found...

Analysis of Tumor Heterogeneity and Cancer Gene Networks Using Deep Sequencing of MMTV-Induced Mouse Mammary Tumors

Cancer develops through a multistep process in which normal cells progress to malignant tumors via the evolution of their genomes as a result of the acquisition of mutations in cancer driver genes. The number, identity and mode of action of cancer driver genes, and how they contribute to tumor evolution is largely unknown. This study deployed the Mouse Mammary Tumor Virus (MMTV...