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https://www.readbyqxmd.com/read/29672640/differential-impact-of-transplantation-on-peripheral-and-tissue-associated-viral-reservoirs-implications-for-hiv-gene-therapy
#1
Christopher W Peterson, Jianbin Wang, Claire Deleage, Sowmya Reddy, Jasbir Kaur, Patricia Polacino, Andreas Reik, Meei-Li Huang, Keith R Jerome, Shiu-Lok Hu, Michael C Holmes, Jacob D Estes, Hans-Peter Kiem
Autologous transplantation and engraftment of HIV-resistant cells in sufficient numbers should recapitulate the functional cure of the Berlin Patient, with applicability to a greater number of infected individuals and with a superior safety profile. A robust preclinical model of suppressed HIV infection is critical in order to test such gene therapy-based cure strategies, both alone and in combination with other cure strategies. Here, we present a nonhuman primate (NHP) model of latent infection using simian/human immunodeficiency virus (SHIV) and combination antiretroviral therapy (cART) in pigtail macaques...
April 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29668265/receptor-mediated-delivery-of-crispr-cas9-endonuclease-for-cell-type-specific-gene-editing
#2
Romain Rouet, Benjamin A Thuma, Marc D Roy, Nathanael G Lintner, David M Rubitski, James E Finley, Hanna M Wisniewska, Rima Mendonsa, Ariana Hirsh, Lorena de Oñate, Joan Compte, Thomas J Mclellan, Justin Bellenger, Xidong Feng, Alison Varghese, Boris A Chrunyk, Kris A Borzilleri, Kevin D Hesp, Kaihong Zhou, Nannan Ma, Meihua Tu, Robert Dullea, Kim F Mcclure, Ross C Wilson, Spiros Liras, Vincent Mascitti, Jennifer A Doudna
CRISPR-Cas RNA-guided endonucleases hold great promise for disrupting or correcting genomic sequences through site-specific DNA cleavage and repair. However, the lack of methods for cell- and tissue-selective delivery currently limits both research and clinical uses of these enzymes. We report the design and in vitro evaluation of S. pyogenes Cas9 proteins harboring asialoglycoprotein receptor ligands (ASGPrL). In particular, we demonstrate that the resulting ribonucleoproteins (Cas9-ASGPrL RNP) can be engineered to be preferentially internalized into cells expressing the corresponding receptor on their surface...
April 18, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29662087/accurate-identification-of-rna-editing-sites-from-primitive-sequence-with-deep-neural-networks
#3
Zhangyi Ouyang, Feng Liu, Chenghui Zhao, Chao Ren, Gaole An, Chuan Mei, Xiaochen Bo, Wenjie Shu
RNA editing is a post-transcriptional RNA sequence alteration. Current methods have identified editing sites and facilitated research but require sufficient genomic annotations and prior-knowledge-based filtering steps, resulting in a cumbersome, time-consuming identification process. Moreover, these methods have limited generalizability and applicability in species with insufficient genomic annotations or in conditions of limited prior knowledge. We developed DeepRed, a deep learning-based method that identifies RNA editing from primitive RNA sequences without prior-knowledge-based filtering steps or genomic annotations...
April 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29661116/crispr-cas9-targeted-deletion-of-polyglutamine-in-spinocerebellar-ataxia-type-3-derived-induced-pluripotent-stem-cells
#4
Shuming Ouyang, Yingjun Xie, Zeyu Xiong, Yi Yang, Yexing Xian, Zhanhui Ou, Bing Song, Yuchang Chen, Yuhuan Xie, Haoxian Li, Xiaofang Sun
Spinocerebellar ataxia type 3 (SCA3) is caused by an abnormal expansion of the CAG triplet in ATXN3, which translates into a polyglutamine (polyQ) tract within ataxin-3 (ATXN3) protein. Although the pathogenic mechanisms remain unclear, it is well established that expression of mutant forms of ATXN3 carrying an expanded polyQ domain are involved in SCA3 pathogenesis, and several strategies to suppress mutant ATXN3 have showed promising potential for SCA3 treatment. In this study, we described successful CRISPR/Cas9-mediated deletion of the expanded polyQ-encoding region of ATXN3 in induced pluripotent stem cells (iPSCs) derived from a SCA3 patient, and these patient-specific iPSCs retained pluripotency and neural differentiation following expanded polyQ deletion...
April 17, 2018: Stem Cells and Development
https://www.readbyqxmd.com/read/29660180/a-chromatin-loop-represses-wuschel-expression-in-arabidopsis
#5
Lin Guo, Xiuwei Cao, Yuhao Liu, Jun Li, Yongpeng Li, Dongming Li, Ke Zhang, Caixia Gao, Aiwu Dong, Xigang Liu
WUSCHEL (WUS) is critical for plant meristem maintenance and determinacy in Arabidopsis, and the regulation of its spatiotemporal expression patterns is complex. We previously found that AGAMOUS (AG), a key MADS-domain transcription factor in floral organ identity and floral meristem determinacy, can directly suppress WUS expression through the recruitment of the Polycomb group (PcG) protein TERMINAL FLOWER2 (TFL2, also known as LIKE HETEROCHROMATIN PROTEIN1, LHP1) at the WUS locus. However, the mechanism by which WUS is repressed remains unclear...
April 16, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29659719/pysster-classification-of-biological-sequences-by-learning-sequence-and-structure-motifs-with-convolutional-neural-networks
#6
Stefan Budach, Annalisa Marsico
Summary: Convolutional neural networks (CNNs) have been shown to perform exceptionally well in a variety of tasks, including biological sequence classification. Available implementations, however, are usually optimized for a particular task and difficult to reuse. To enable researchers to utilize these networks more easily we implemented pysster, a Python package for training CNNs on biological sequence data. Sequences are classified by learning sequence and structure motifs and the package offers an automated hyper-parameter optimization procedure and options to visualize learned motifs along with information about their positional and class enrichment...
April 6, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29651774/genome-editing-for-the-treatment-of-tumorigenic-viral-infections-and-virus-related-carcinomas
#7
REVIEW
Lan Yu, Xun Tian, Chun Gao, Ping Wu, Liming Wang, Bei Feng, Xiaomin Li, Hui Wang, Ding Ma, Zheng Hu
Viral infections cause at least 10%-15% of all human carcinomas. Over the last century, the elucidation of viral oncogenic roles in many cancer types has provided fundamental knowledge on carcinogenetic mechanisms and established a basis for the early intervention of virus-related cancers. Meanwhile, rapidly evolving genomeediting techniques targeting viral DNA/RNA have emerged as novel therapeutic strategies for treating virusrelated carcinogenesis and have begun showing promising results. This review discusses the recent advances of genome-editing tools for treating tumorigenic viruses and their corresponding cancers, the challenges that must be overcome before clinically applying such genome-editing technologies, and more importantly, the potential solutions to these challenges...
April 12, 2018: Frontiers of Medicine
https://www.readbyqxmd.com/read/29650777/-mll-leukemia-induction-by-t-9-11-chromosomal-translocation-in-human-hematopoietic-stem-cells-using-genome-editing
#8
Corina Schneidawind, Johan Jeong, Dominik Schneidawind, In-Suk Kim, Jesús Duque-Afonso, Stephen Hon Kit Wong, Masayuki Iwasaki, Erin H Breese, James L Zehnder, Matthew Porteus, Michael L Cleary
Genome editing provides a potential approach to model de novo leukemogenesis in primary human hematopoietic stem and progenitor cells (HSPCs) through induction of chromosomal translocations by targeted DNA double-strand breaks. However, very low efficiency of translocations and lack of markers for translocated cells serve as barriers to their characterization and model development. Here, we used transcription activator-like effector nucleases to generate t(9;11) chromosomal translocations encoding MLL-AF9 and reciprocal AF9-MLL fusion products in CD34+ human cord blood cells...
April 24, 2018: Blood Advances
https://www.readbyqxmd.com/read/29650679/real-time-observation-of-flexible-domain-movements-in-crispr-cas9
#9
Saki Osuka, Kazushi Isomura, Shohei Kajimoto, Tomotaka Komori, Hiroshi Nishimasu, Tomohiro Shima, Osamu Nureki, Sotaro Uemura
The CRISPR-associated protein Cas9 is widely used for genome editing because it cleaves target DNA through the assistance of a single-guide RNA (sgRNA). Structural studies have revealed the multi-domain architecture of Cas9 and suggested sequential domain movements of Cas9 upon binding to the sgRNA and the target DNA These studies also hinted at the flexibility between domains; however, it remains unclear whether these flexible movements occur in solution. Here, we directly observed dynamic fluctuations of multiple Cas9 domains, using single-molecule FRET We found that the flexible domain movements allow Cas9 to adopt transient conformations beyond those captured in the crystal structures...
April 12, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29650467/chemically-modified-cpf1-crispr-rnas-mediate-efficient-genome-editing-in-mammalian-cells
#10
Moira A McMahon, Thazha P Prakash, Don W Cleveland, C Frank Bennett, Meghdad Rahdar
CRISPR-based gene editing is a powerful technology for engineering mammalian genomes. It holds the potential as a therapeutic, although much-needed in vivo delivery systems have yet to be established. Here, using the Cpf1-crRNA (CRISPR RNA) crystal structure as a guide, we synthesized a series of systematically truncated and chemically modified crRNAs, and identify positions that are amenable to modification while retaining gene-editing activity. Modified crRNAs were designed with the same modifications that provide protection against nucleases and enable wide distribution in vivo...
March 6, 2018: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/29649127/gene-therapy-for-chronic-hbv-can-we-eliminate-cccdna
#11
REVIEW
Kristie Bloom, Mohube Betty Maepa, Abdullah Ely, Patrick Arbuthnot
Chronic infection with the hepatitis B virus (HBV) is a global health concern and accounts for approximately 1 million deaths annually. Amongst other limitations of current anti-HBV treatment, failure to eliminate the viral covalently closed circular DNA (cccDNA) and emergence of resistance remain the most worrisome. Viral rebound from latent episomal cccDNA reservoirs occurs following cessation of therapy, patient non-compliance, or the development of escape mutants. Simultaneous viral co-infections, such as by HIV-1, further complicate therapeutic interventions...
April 12, 2018: Genes
https://www.readbyqxmd.com/read/29648606/ecd1-functions-as-an-rna-editing-trans-factor-of-rps14-149-in-plastids-and-is-required-for-early-chloroplast-development
#12
Tian Jiang, Jing Zhang, Liwei Rong, Yanjiang Feng, Qi Wang, Qiulai Song, Lixin Zhang, Min Ouyang
Chloroplast development is a highly complex process and the regulatory mechanism has not been fully characterized. Identification of the corresponding regulators will shed light on the intricacies of chloroplast development. Here, we identified ECD1 (Early Chloroplast Development 1), a chloroplast-localized pentatricopeptide repeat protein (PPR) belonging to the PLS subfamily. Inactivation of ECD1 leads to embryo lethality, and abnormal embryogenesis occurs in ecd1/+ heterozygous plants. A decrease of ECD1 induced by RNA interference (RNAi) results in seedlings with albino cotyledons but normal true leaves...
April 10, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29644996/simultaneous-lineage-tracing-and-cell-type-identification-using-crispr-cas9-induced-genetic-scars
#13
Bastiaan Spanjaard, Bo Hu, Nina Mitic, Pedro Olivares-Chauvet, Sharan Janjuha, Nikolay Ninov, Jan Philipp Junker
A key goal of developmental biology is to understand how a single cell is transformed into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the developmental origin of cells remains challenging. Here we present LINNAEUS (lineage tracing by nuclease-activated editing of ubiquitous sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells...
April 9, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29644494/review-of-crispr-cas9-sgrna-design-tools
#14
REVIEW
Yingbo Cui, Jiaming Xu, Minxia Cheng, Xiangke Liao, Shaoliang Peng
The adaptive immunity system in bacteria and archaea, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-associate (CRISPR/Cas), has been adapted as a powerful gene editing tool and got a broad application in genome research field due to its ease of use and cost-effectiveness. The performance of CRISPR/Cas relies on well-designed single-guide RNA (sgRNA), so a lot of bioinformatic tools have been developed to assist the design of highly active and specific sgRNA. These tools vary in design specifications, parameters, genomes and so on...
April 11, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29642585/mitochondrial-biogenesis-in-diverse-cauliflower-cultivars-under-mild-and-severe-drought-impaired-coordination-of-selected-transcript-and-proteomic-responses-and-regulation-of-various-multifunctional-proteins
#15
Michał Rurek, Magdalena Czołpińska, Tomasz Andrzej Pawłowski, Aleksandra Maria Staszak, Witold Nowak, Włodzimierz Krzesiński, Tomasz Spiżewski
Mitochondrial responses under drought within Brassica genus are poorly understood. The main goal of this study was to investigate mitochondrial biogenesis of three cauliflower ( Brassica oleracea var. botrytis ) cultivars with varying drought tolerance. Diverse quantitative changes (decreases in abundance mostly) in the mitochondrial proteome were assessed by two-dimensional gel electrophoresis (2D PAGE) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Respiratory (e.g., complex II, IV (CII, CIV) and ATP synthase subunits), transporter (including diverse porin isoforms) and matrix multifunctional proteins (e...
April 10, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29625900/adar1-and-pkr-interferon-stimulated-genes-with-clashing-effects-on-hiv-1-replication
#16
REVIEW
Roman Radetskyy, Aïcha Daher, Anne Gatignol
The induction of hundreds of Interferon Stimulated Genes (ISGs) subsequent to virus infection generates an antiviral state that functions to restrict virus growth at multiple steps of their replication cycles. In the context of Human Immunodeficiency Virus-1 (HIV-1), ISGs also possess antiviral functions, but some ISGs show proapoptotic or proviral activity. One of the most studied ISGs, the RNA activated Protein Kinase (PKR), shuts down the viral protein synthesis upon activation. HIV-1 has evolved to evade its inhibition by PKR through viral and cellular mechanisms...
March 26, 2018: Cytokine & Growth Factor Reviews
https://www.readbyqxmd.com/read/29625544/identification-of-single-amino-acid-substitutions-in-proteogenomics
#17
REVIEW
S A Moshkovskii, M V Ivanov, K G Kuznetsova, M V Gorshkov
An important aim of proteogenomics, which combines data of high throughput nucleic acid and protein analysis, is to reliably identify single amino acid substitutions representing a main type of coding genome variants. Exact knowledge of deviations from the consensus genome can be utilized in several biomedical fields, such as studies of expression of mutated proteins in cancer, deciphering heterozygosity mechanisms, identification of neoantigens in anticancer vaccine production, search for RNA editing sites at the level of the proteome, etc...
March 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29625203/crispys-optimal-sgrna-design-for-editing-multiple-members-of-a-gene-family-using-the-crispr-system
#18
Gal Hyams, Shiran Abadi, Shlomtzion Lahav, Adi Avni, Eran Halperin, Eilon Shani, Itay Mayrose
The development of the CRISPR-Cas9 system in recent years has made eukaryotic genome editing, and specifically gene knockout for reverse genetics, a simple and effective task. The system is directed to a genomic target site by a programmed single-guide RNA (sgRNA) that base-pairs with it, subsequently leading to site-specific modifications. However, many gene families in eukaryotic genomes exhibit partially overlapping functions and, thus, the knockout of one gene might be concealed by the function of the other...
April 3, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29623532/genome-editing-in-induced-pluripotent-stem-cells-using-crispr-cas9
#19
REVIEW
Ronen Ben Jehuda, Yuval Shemer, Ofer Binah
The development of the reprogramming technology led to generation of induced Pluripotent Stem Cells (iPSC) from a variety of somatic cells. Ever since, fast growing knowledge of different efficient protocols enabled the differentiation of these iPSCs into different cells types utilized for disease modeling. Indeed, iPSC-derived cells have been increasingly used for investigating molecular and cellular pathophysiological mechanisms underlying inherited diseases. However, a major barrier in the field of iPSC-based disease modeling relies on discriminating between the effects of the causative mutation and the genetic background of these cells...
April 6, 2018: Stem Cell Reviews
https://www.readbyqxmd.com/read/29621707/identification-of-cd-responsive-rna-helicase-genes-and-expression-of-a-putative-bnrh-24-mediated-by-mir158-in-canola-brassica-napus
#20
Xian Duo Zhang, Jia Yun Sun, Yuan Yuan You, Jian Bo Song, Zhi Min Yang
RNA helicases play crucial roles in RNA splicing, transport, editing and degradation, protein translation initiation and siRNA-mediated gene silencing. However, knowledge about their functionality in rapeseed (Brassica napus) is rare. In the study, we identified and annotated 271 RNA helicase genes from B. napus using bioinformatics and high-throughput RNA-sequencing (RNA-seq). Three subfamilies DEAD-box, DEAH-box, or DExD/H-box have been identified. One hundred and ninety-five RNA helicases were confirmed by RNA-seq and 49 were identified to differentially respond to cadmium (Cd) stress (> 1...
April 2, 2018: Ecotoxicology and Environmental Safety
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