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AMOD: a morpholino oligonucleotide selection tool

E. W. Klee, K. J. Shim, M. A. Pickart, S. C. Ekker, L. B. M. Ellis
2005 Nucleic Acids Research  
AMOD is a web-based program that aids in the functional evaluation of nucleotide sequences through sequence characterization and antisense morpholino oligonucleotide (target site) selection.  ...  Within a defined subsequence, base composition and homodimerization values are computed for all putative morpholino oligonucleotides.  ...  This work was supported in part by NIH R01-GM63904, a predoctoral traineeship to E.K. (NLM TG-0704l), and a postdoctoral traineeship to M.A.P. (NIDCR: T32 DE07288-8).  ... 
doi:10.1093/nar/gki453 pmid:15980523 pmcid:PMC1160214 fatcat:3ozsd5mnv5cbpmmrgkk2u7a4ru

A Primer for Morpholino Use in Zebrafish

Brent R. Bill, Andrew M. Petzold, Karl J. Clark, Lisa A. Schimmenti, Stephen C. Ekker
2009 Zebrafish  
Morpholino oligonucleotides are the most common anti-sense "knockdown" technique used in zebrafish (Danio rerio).  ...  Off-targeting effects of morpholinos are discussed as well as method to minimize this potentially confounding variable via co-injection of a tP53-targeting morpholino.  ...  Disclosure Statement The authors have no financial affiliation with any research supplier in this article, notably including Gene-Tools LLC.  ... 
doi:10.1089/zeb.2008.0555 pmid:19374550 pmcid:PMC2776066 fatcat:kzhrjjhd4jghtdjlj3dxj67auq

Genome-Wide Reverse Genetics Framework to Identify Novel Functions of the Vertebrate Secretome

Michael A. Pickart, Eric W. Klee, Aubrey L. Nielsen, Sridhar Sivasubbu, Eric M. Mendenhall, Brent R. Bill, Eleanor Chen, Craig E. Eckfeldt, Michelle Knowlton, Mara E. Robu, Jon D. Larson, Yun Deng (+7 others)
2006 PLoS ONE  
This study provides a framework utilizing zebrafish for the systematic assignment of biological function in a vertebrate genome.  ...  We further investigated 150 of these genes ( Figure 1 ) for unique function using morpholino-based analysis in zebrafish embryos. 12% of the CTT protein-deficient embryos resulted in specific developmental  ...  Morpholino phosphorodiamidate oligonucleotides (MOs), neutrally charged nucleic acid analogs created by replacing the ribose sugar with a morpholine moiety and the phosophodiester backbone with a phosphorodiamidate  ... 
doi:10.1371/journal.pone.0000104 pmid:17218990 pmcid:PMC1766371 fatcat:4ujokztgxrddhnd5e4sonjfvwa

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information

Michelle N Knowlton, Tongbin Li, Yongliang Ren, Brent R Bill, Lynda BM Ellis, Stephen C Ekker
2008 BMC Bioinformatics  
We have created a database to facilitate web-based distribution of data from such genetic studies. Description: The MOrpholino DataBase is a MySQL relational database with an online, PHP interface.  ...  To improve the searchability of this database, we have incorporated a fixed-vocabulary defect ontology that allows for the organization of morpholino affects based on anatomical structure affected and  ...  for morpholino design, carried out using an Assisted MOrpholino Design tool (AMOD) [11, 12] .  ... 
doi:10.1186/1471-2105-9-7 pmid:18179718 pmcid:PMC2221974 fatcat:6jsytilfcbcvtijgow3vl2jivu

Defining Synphenotype Groups in Xenopus tropicalis by Use of Antisense Morpholino Oligonucleotides

Amer Ahmed Rana, Clara Collart, Michael J. Gilchrist, J. C. Smith
2006 PLoS Genetics  
To identify novel genes involved in early development, and as proof-of-principle of a large-scale reverse genetics approach in a vertebrate embryo, we have carried out an antisense morpholino oligonucleotide  ...  Citation: Rana AA, Collart C, Gilchrist MJ, Smith JC (2006) Defining synphenotype groups in Xenopus tropicalis by use of antisense morpholino oligonucleotides. PLoS Genet 2(11): e193.  ...  In the future it will be helpful to have a tool such as AMOD [26] to help in the design of X. tropicalis MOs.  ... 
doi:10.1371/journal.pgen.0020193 pmid:17112317 pmcid:PMC1636699 fatcat:iczaj3pptbffdb6aruwm25fo7y

Defining Synphenotype Groups in Xenopus tropicalis by Use of Antisense Morpholino Oligonucleotides

Amer Rana, Clara Collart, Michael Gilchrist, Jim Smith
2005 PLoS Genetics  
To identify novel genes involved in early development, and as proof-of-principle of a large-scale reverse genetics approach in a vertebrate embryo, we have carried out an antisense morpholino oligonucleotide  ...  Analysis of the expression patterns of the 202 genes indicates that members of a synphenotype group are not necessarily members of the same synexpression group.  ...  In the future it will be helpful to have a tool such as AMOD [26] to help in the design of X. tropicalis MOs.  ... 
doi:10.1371/journal.pgen.0020193.eor fatcat:cfbnp7ucr5a43ec2xn53bu6liu

Abstracts of the 10th International Conference on Cachexia, Sarcopenia and Muscle Wasting, Rome, Italy, 8-10 December 2017 (Part 1)

2017 Journal of Cachexia, Sarcopenia and Muscle  
The majority of the participants has decreased SMM, SMI and BMI and increased WHR, which favors a worst prognostic for comorbidities associated with these variables, and a tendency for sarcopenic obesity  ...  Results: A significant difference was found over three years in SMM (p = 0.007), SMI (p = 0.027), BMI (p = 0.041) and WHR (p = 0.003).  ...  as a sarcopenia screening tool in a Brazilian population Thiago G.  ... 
doi:10.1002/jcsm.12255 fatcat:cxx5afjdpvb2pfmzy35jiwes4a

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016): part two

Casey Ager, Matthew Reilley, Courtney Nicholas, Todd Bartkowiak, Ashvin Jaiswal, Michael Curran, Tina C. Albershardt, Anshika Bajaj, Jacob F. Archer, Rebecca S. Reeves, Lisa Y. Ngo, Peter Berglund (+1790 others)
2016 Journal for ImmunoTherapy of Cancer  
Acknowledgements Gene expression data from melanoma metastases were provided by Steven A Rosenberg (NCI).  ...  murine model of pancreatic cancer Shari Pilon-Thomas, Amy Weber, Jennifer Morse, Krithika Kodumudi, Hao Liu, John Mullinax, Amod A Sarnaik H.  ...  , or the combination of CTLA-4 antibody and CD47 morpholino.  ... 
doi:10.1186/s40425-016-0173-6 fatcat:pst7b6kmyral7ihb6esgw53goq

Generation of novel developmental and adult zebrafish models of amyotrophic lateral sclerosis

Alison Hogan
2022
Zebrafish have emerged as useful tools to identify and investigate mechanisms of human disease.  ...  Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterisedby the death of upper and lower motor neurons.  ...  Acknowledgements "A Ph.D is an exhausting, emotional struggle. You are forced to confront all of your fears, insecurities and doubts you have about yourself and somehow overcome them.  ... 
doi:10.25949/19433576.v1 fatcat:lvtqmvealnbppasa3izaivunpu