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Crispr-cas9

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https://www.readbyqxmd.com/read/29053735/characterization-of-the-first-knock-out-aldh7a1-zebrafish-model-for-pyridoxine-dependent-epilepsy-using-crispr-cas9-technology
#1
Nikita Zabinyakov, Garrett Bullivant, Feng Cao, Matilde Fernandez Ojeda, Zheng Ping Jia, Xiao-Yan Wen, James J Dowling, Gajja S Salomons, Saadet Mercimek-Andrews
Pyridoxine dependent epilepsy (PDE) is caused by likely pathogenic variants in ALDH7A1 (PDE-ALDH7A1) and inherited autosomal recessively. Neurotoxic alpha-amino adipic semialdehyde (alpha-AASA), piperideine 6-carboxylate and pipecolic acid accumulate in body fluids. Neonatal or infantile onset seizures refractory to anti-epileptic medications are clinical features. Treatment with pyridoxine, arginine and lysine-restricted diet does not normalize neurodevelopmental outcome or accumulation of neurotoxic metabolites...
2017: PloS One
https://www.readbyqxmd.com/read/29051769/osgif1-positively-regulates-the-sizes-of-stems-leaves-and-grains-in-rice
#2
Zhongshan He, Jing Zeng, Yun Ren, Dan Chen, Wenjie Li, Fengyan Gao, Ye Cao, Tao Luo, Guoqiang Yuan, Xianghong Wu, Yueyang Liang, Qiming Deng, Shiquan Wang, Aiping Zheng, Jun Zhu, Huainian Liu, Lingxia Wang, Ping Li, Shuangcheng Li
Growth-regulating factor (GRF) interacting factors (GIFs) are involved in several developmental processes in Arabidopsis. We previously showed that upregulation of OsGIF1 expression improves rice grain size. However, whether OsGIF1 is involved in other developmental processes remains unclear. Here, we report pleiotropic effects of OsGIF1 on rice organ size regulation. Overexpression and functional knock-out via a CRISPR/Cas9 strategy revealed that OsGIF1 not only positively regulates the sizes of rice leaf, stem, and grain but also influences rice reproduction...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29051389/new-genes-often-acquire-male-specific-functions-but-rarely-become-essential-in-drosophila
#3
Shu Kondo, Jeffrey Vedanayagam, Jaaved Mohammed, Sogol Eizadshenass, Lijuan Kan, Nan Pang, Rajaguru Aradhya, Adam Siepel, Josefa Steinhauer, Eric C Lai
Relatively little is known about the in vivo functions of newly emerging genes, especially in metazoans. Although prior RNAi studies reported prevalent lethality among young gene knockdowns, our phylogenomic analyses reveal that young Drosophila genes are frequently restricted to the nonessential male reproductive system. We performed large-scale CRISPR/Cas9 mutagenesis of "conserved, essential" and "young, RNAi-lethal" genes and broadly confirmed the lethality of the former but the viability of the latter...
September 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/29051387/out-of-the-testis-biological-impacts-of-new-genes
#4
REVIEW
Kevin G Nyberg, Richard W Carthew
The study of newly evolved genes has long fascinated biologists, but large-scale studies of their expression dynamics and molecular function have provided conflicting interpretations of their biological impact. In this issue of Genes & Development, Kondo and colleagues (pp. 1841-1846) use extensive transcriptomic resources and current CRISPR/Cas9 technology to re-examine the functional impact of newly evolved genes in Drosophila and find evidence of their biological impact on male reproduction.
September 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/29051223/crispr-cas9-based-screening-of-long-noncoding-rnas-lncrnas-in-macrophages-with-an-nf-kappa-b-reporter
#5
Sergio Covarrubias, Elektra K Robinson, Barbara Shapleigh, Apple Vollmers, Solomon Katzman, Nicole Hanley, Nicholas Fong, Michael T McManus, Susan Carpenter
The innate immune system protects against infections by initiating an inducible inflammatory response. NF-kappa B (NF-KB) is one of the critical transcription factors controlling this complex response, but some aspects of its regulation remain unclear. For example, although long noncoding RNAs (lncRNAs) have been shown to critically regulate gene expression, only a fraction of these have been functionally characterized, and the extent to which lncRNAs control NF-KB expression is unknown. Here, we describe the generation of a GFP-based NF-KB reporter system in immortalized murine bone marrow-derived macrophages (iBMDMs)...
October 19, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29051052/pea-early-browning-virus-mediated-genome-editing-via-the-crispr-cas9-system-in-nicotiana-benthamiana-and-arabidopsis
#6
Zahir Ali, Ayman Eid, Shakila Ali, Magdy M Mahfouz
The clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system has enabled efficient genome engineering in diverse plant species. However, delivery of genome engineering reagents, such as the single guide RNA (sgRNA), into plant cells remains challenging. Here, we report the engineering of Tobacco rattle virus (TRV) and Pea early browning virus (PEBV) to deliver one or multiple sgRNAs into Nicotiana benthamiana and Arabidopsis thaliana (Col-0) plants that overexpress a nuclear localization signal containing Cas9...
October 16, 2017: Virus Research
https://www.readbyqxmd.com/read/29050985/bromodomain-protein-brd4-promotes-cell-proliferation-in-skin-squamous-cell-carcinoma
#7
Tie Xiang, Jin-Yu Bai, Cang She, Dao-Jiang Yu, Xiao-Zhong Zhou, Tian-Lan Zhao
The present study examined the expression and biological functions of bromodomain-containing protein 4 (BRD4) in skin squamous cell carcinoma (SCC) cells. Our results show that BRD4 mRNA and protein expression was upregulated in human skin SCC cells, as compared to its level in the normal skin keratinocytes and fibroblasts. Treatment with BRD4 inhibitors, JQ1 and CPI203, resulted in proliferation inhibition, apoptosis and cell cycle arrest in both established (A431 cell line) and primary skin SCC cells. Furthermore, BRD4 knockdown (by targeted shRNAs) or knockout (by CRISPR/Cas9) largely inhibited A431 cell proliferation...
October 16, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/29050200/targeting-muc1-c-suppresses-polycomb-repressive-complex-1-in-multiple-myeloma
#8
Ashujit Tagde, Tahireh Markert, Hasan Rajabi, Masayuki Hiraki, Maroof Alam, Audrey Bouillez, David Avigan, Kenneth Anderson, Donald Kufe
The polycomb repressive complex 1 (PRC1) includes the BMI1, RING1 and RING2 proteins. BMI1 is required for survival of multiple myeloma (MM) cells. The MUC1-C oncoprotein is aberrantly expressed by MM cells, activates MYC and is also necessary for MM cell survival. The present studies show that targeting MUC1-C with (i) stable and inducible silencing and CRISPR/Cas9 editing and (ii) the pharmacologic inhibitor GO-203, which blocks MUC1-C function, downregulates BMI1, RING1 and RING2 expression. The results demonstrate that MUC1-C drives BMI1 transcription by a MYC-dependent mechanism...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29046446/foamy-virus-vector-carries-a-strong-insulator-in-its-long-terminal-repeat-which-reduces-its-genotoxic-potential
#9
Michael A Goodman, Paritha I Arumugam, Devin M Pillis, Anastacia Loberg, Md Nasimuzzaman, Danielle Lynn, Johannes C M van der Loo, Phillip J Dexheimer, Mehdi Keddache, Thomas R Bauer, Dennis D Hickstein, David W Russell, Punam Malik
Strong viral enhancers in γ-retrovirus vectors have caused cellular proto-oncogene activation and leukemia, necessitating use of cellular promoters in 'enhancer-less' self-inactivating integrating vectors. However, cellular promoters result in relatively low transgene expression, often leading to inadequate disease correction. Vectors derived from foamy virus, a nonpathogenic retrovirus, show higher preference for non-genic integrations than γ-retroviruses/lentiviruses and preferential integration near transcriptional start sites, like γ-retroviruses...
October 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29046337/cathepsin-b-is-dispensable-for-cellular-processing-of-cathepsin-b-cleavable-antibody-drug-conjugates
#10
Niña G Caculitan, Josefa Dela Cruz Chuh, Yong Ma, Donglu Zhang, Katherine R Kozak, Yichin Liu, Thomas H Pillow, Jack Sadowsky, Tommy K Cheung, Qui Phung, Benjamin Haley, Byoung-Chul Lee, Robert Akita, Mark X Sliwkowski, Andrew G Polson
Antibody-drug conjugates (ADCs) are designed to selectively bind to tumor antigens via the antibody and release their cytotoxic payload upon internalization. Controllable payload release through judicious design of the linker has been an early technological milestone. Here, we examine the effect of the protease-cleavable valine-citrulline (VC(S)) linker on ADC efficacy. The VC(S) linker was designed to be cleaved by cathepsin B, a lysosomal cysteine protease. Surprisingly, suppression of cathepsin B expression via CRISPR-Cas9 gene deletion or shRNA knockdown had no effect on the efficacy of ADCs with VC(S) linkers armed with a monomethyl auristatin E (MMAE) payload...
October 18, 2017: Cancer Research
https://www.readbyqxmd.com/read/29046334/the-organic-anion-transporter-slco2a1-constitutes-the-core-component-of-the-maxi-cl-channel
#11
Ravshan Z Sabirov, Petr G Merzlyak, Toshiaki Okada, Md Rafiqul Islam, Hiromi Uramoto, Tomoko Mori, Yumiko Makino, Hiroshi Matsuura, Yu Xie, Yasunobu Okada
The maxi-anion channels (MACs) are expressed in cells from mammals to amphibians with ~60% exhibiting a phenotype called Maxi-Cl. Maxi-Cl serves as the most efficient pathway for regulated fluxes of inorganic and organic anions including ATP However, its molecular entity has long been elusive. By subjecting proteins isolated from bleb membranes rich in Maxi-Cl activity to LC-MS/MS combined with targeted siRNA screening, CRISPR/Cas9-mediated knockout, and heterologous overexpression, we identified the organic anion transporter SLCO2A1, known as a prostaglandin transporter (PGT), as a key component of Maxi-Cl...
October 18, 2017: EMBO Journal
https://www.readbyqxmd.com/read/29045831/usp7-is-a-tumor-specific-wnt-activator-for-apc-mutated-colorectal-cancer-by-mediating-%C3%AE-catenin-deubiquitination
#12
Laura Novellasdemunt, Valentina Foglizzo, Laura Cuadrado, Pedro Antas, Anna Kucharska, Vesela Encheva, Ambrosius P Snijders, Vivian S W Li
The tumor suppressor gene adenomatous polyposis coli (APC) is mutated in most colorectal cancers (CRCs), resulting in constitutive Wnt activation. To understand the Wnt-activating mechanism of the APC mutation, we applied CRISPR/Cas9 technology to engineer various APC-truncated isogenic lines. We find that the β-catenin inhibitory domain (CID) in APC represents the threshold for pathological levels of Wnt activation and tumor transformation. Mechanistically, CID-deleted APC truncation promotes β-catenin deubiquitination through reverse binding of β-TrCP and USP7 to the destruction complex...
October 17, 2017: Cell Reports
https://www.readbyqxmd.com/read/29044927/knock-out-of-histamine-receptor-h3-alters-adaptation-to-sudden-darkness-and-monoamine-levels-in-the-zebrafish
#13
Henri A J Puttonen, Maria Sundvik, Svetlana Semenova, Yukako Shirai, Yu-Chia Chen, Pertti Panula
AIM: Histamine receptor H3 has substantial neuropharmacological potential. Currently, knock-out models of this receptor have been investigated only in mice. We characterized the expression of this receptor in the zebrafish and generated a zebrafish histamine receptor H3 knock-out line. Using this model, we studied the role of histamine receptor H3 in important behaviours. We also analyzed the effect of histamine receptor H3 knock-out on monoaminergic systems, which has not been thoroughly studied in any animal model...
October 16, 2017: Acta Physiologica
https://www.readbyqxmd.com/read/29044507/tieg-and-estrogen-modulate-sost-expression-in-the-murine-skeleton
#14
Malayannan Subramaniam, Kevin S Pitel, Elizabeth S Bruinsma, David G Monroe, John R Hawse
TIEG knockout (KO) mice exhibit a female-specific osteopenic phenotype and altered expression of TIEG in humans is associated with osteoporosis. Gene expression profiling studies identified sclerostin as one of the most highly up-regulated transcripts in the long bones of TIEG KO mice relative to WT littermates suggesting that TIEG may regulate SOST expression. TIEG was shown to substantially suppress SOST promoter activity and the regulatory elements through which TIEG functions were identified using promoter deletion and chromatin immunoprecipitation assays...
October 16, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29044017/-crispr-cas9-and-gene-therapy
#15
Luciana E Giono
The development of techniques that allow the precise and efficient edition of the genome of living cells is one of the main goals of biomedical research. Over the last few decades, a number of genome editing tools have been developed, the most prominent being the CRISPR/Cas9 system, a bacterial defense mechanism that has been redesigned for its use in other cellular systems. The accessibility, both technical and economical, and the enormous potential of CRISPR/Cas9 have contributed to an almost unprecedented revolution in the biomedical sciences and represent an important step forward in the field of gene therapy that needs, however, to be taken cautiously...
2017: Medicina
https://www.readbyqxmd.com/read/29043647/the-cellclamper-a-convenient-microfluidic-device-for-time-lapse-imaging-of-yeast
#16
Gregor W Schmidt, Olivier Frey, Fabian Rudolf
Time-lapse fluorescence imaging of yeast cells allows the study of multiple fluorescent targets in single cells, but is often hampered by the tedious cultivation using agar pads or glass bottom wells. Here, we describe the fabrication and operation of a microfluidic device for long-term imaging of yeast cells under constant or changing media conditions. The device allows acquisition of high quality images as cells are fixed in a two-dimensional imaging plane. Four yeast strains can be analyzed simultaneously over several days while up to four different media can be flushed through the chip...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29042517/control-of-growth-and-gut-maturation-by-hoxd-genes-and-the-associated-lncrna-haglr
#17
Jozsef Zakany, Fabrice Darbellay, Bénédicte Mascrez, Anamaria Necsulea, Denis Duboule
During embryonic development, Hox genes participate in the building of a functional digestive system in metazoans, and genetic conditions involving these genes lead to important, sometimes lethal, growth retardation. Recently, this phenotype was obtained after deletion of Haglr, the Hoxd antisense growth-associated long noncoding RNA (lncRNA) located between Hoxd1 and Hoxd3 In this study, we have analyzed the function of Hoxd genes in delayed growth trajectories by looking at several nested targeted deficiencies of the mouse HoxD cluster...
October 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29042501/plasmodium-falciparum-calcium-dependent-protein-kinase-2-is-critical-for-male-gametocyte-exflagellation-but-not-essential-for-asexual-proliferation
#18
Abhisheka Bansal, Alvaro Molina-Cruz, Joseph Brzostowski, Jianbing Mu, Louis H Miller
Drug development efforts have focused mostly on the asexual blood stages of the malaria parasite Plasmodium falciparum Except for primaquine, which has its own limitations, there are no available drugs that target the transmission of the parasite to mosquitoes. Therefore, there is a need to validate new parasite proteins that can be targeted for blocking transmission. P. falciparum calcium-dependent protein kinases (PfCDPKs) play critical roles at various stages of the parasite life cycle and, importantly, are absent in the human host...
October 17, 2017: MBio
https://www.readbyqxmd.com/read/29041978/linc-ror-promotes-mapk-erk-signaling-and-confers-estrogen-independent-growth-of-breast-cancer
#19
Wan-Xin Peng, Jian-Guo Huang, Liu Yang, Ai-Hua Gong, Yin-Yuan Mo
BACKGROUND: The conversion from estrogen-dependent to estrogen-independent state of ER+ breast cancer cells is the key step to promote resistance to endocrine therapies. Although the crucial role of MAPK/ERK signaling pathway in estrogen-independent breast cancer cell growth is well established, the underlying mechanism is not fully understood. METHODS: In this study, we profiled lncRNA expression against a focused group of lncRNAs selected from lncRNA database...
October 17, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/29040704/in-planta-processing-of-the-spcas9-grna-complex
#20
Masafumi Mikami, Seiichi Toki, Masaki Endo
In CRISPR/Cas9-mediated genome editing in plants, Streptococcus pyogenes Cas9 (SpCas9) protein and the required guide RNA (gRNA) are, in most cases, expressed from a stably integrated transgene. Generally, SpCas9 protein is expressed from an RNA polymerase (pol) II promoter, while gRNA is expressed from a pol III promoter. However, pol III promoters have not been much characterized other than in model plants, making it difficult to select appropriate promoters for specific applications, while pol II transcripts have to be processed to generate functional gRNAs...
October 12, 2017: Plant & Cell Physiology
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