...Lukas Morgan Model organisms are vital tools used by researchers around the globe. These organisms share...forefront by Thomas Hunt Morgan, who is known as the “father” of Drosophila research. Morgan discovered that genes...one of the simplest eukaryotic organism, is a commonly used model organism in scientific research. Yes, ...Looking for more model organisms? Check out Part two in the popular model organisms series, and read about...this blog post, we’ll cover five popular model organisms, but there are many more out there. The house... start with the most preferred mammalian model organism of many researchers: the mouse (Mus musculus)....Mice have many advantages as a mammalian model organism for scientists as they have a relatively short...

...covered five model organisms in a previous blog post, but here are five more model organisms that have left...emerging model organisms!) Escherichia coli One of the most recognizable and utilized model organisms is Escherichia...as a model organism for over 60 years with a status as the most studied prokaryotic organism. With its ...https://doi.org/10.7554/elife.05826 Blum, M., & Ott, T. (2018). Xenopus: An Undervalued Model Organism to ...Genetic Disease. Cells Tissues Organs, 205(5–6), 303–313. https://doi.org/10.1159/000490898 Gibbs, R., ...amphibian model organisms. Dong wu xue yan jiu = Zoological research, 37(4), 237–245. https://doi.org/10.13918...https://doi.org/10.1038/s41467-018-04899-x Yokoyama, Maho. (2020, May 28). E. coli as a Model Organism. News-Medical...

...responsibilities Being a leader in an organization, you need to make sure the organization speaks in “one voice” whilst...great organization to develop these leadership skills in particular because every year it organized a “Committee...written a 5-part blog on the topic:  http://blog.addgene.org/management-for-scientists-managing-vs-leading... achieved by volunteering for a professional organization or a scientific society in your field. My leadership... in the long run was most beneficial for the organization as a whole. I came to understand that not only...only was I growing as a leader but the organization was growing too and with that would come necessary... had to be professional as I represented the organization, not just myself as a scientist. I learnt to...

...body is made up of organs, cells comprise compartments and structures, called organelles. Take a sneak peak...fluorescent microscopy - even in living cells and whole organisms. You can take advantage of the many Fluorescent... proteins” which are known to be a part of an organelle or involved in intracellular transport pathways...pathways, it is possible to map the internal organization of a cell. This mapping can be done by using antibodies...for commonly used markers for major mammalian organelles and transport pathways. It is best, though not...that traffics the fluorescent protein to your organelle of interest. Click on the gene names in the figure...Cell: A Molecular Approach. 2nd Edition. 3.  CureFFI.org. Cell Biology 04: The Secretory Pathway. 4. Dunn...

...populations of transgenic laboratory organisms but not wild organisms. For example, an sgRNA-only drive ...confinement seeks to keep the organisms in the laboratory. It varies by organism, but your local biosafety... Medical School. Scientists making transgenic organisms with Cas9 should be aware of the potential hazards... can spread even when costly. If even a single organism carrying a synthetic gene drive were to escape... extreme caution. Why does making transgenic organisms with Cas9 risk creating a gene drive? The simplest...idea or wanted to build a gene drive in a model organism would find our work and consequently use these...experiments in a geographic area where escaped organisms won't be able to find mates2. For example, ongoing...

...send you daily updates with relevant literature. Organizing the literature As a scientist, you will begin...will ever read. So, you need to come up with an organization system that works for you. I have a folder where...’m still in the dark ages with respect to my organization strategy. There are a number of software options...another option that may help solve your literature organization issues – F1000 just announced the launch of ....  Give your favorite searching, reading and organization tips in the comments below. Additionally, read...

...next R01 is due. But what about organizing yourself and your lab? Organizing your lab notebooks, protocols...you think! Here are three tips to help you get organized and boost your productivity in 2014. Tip 1: Use...and no closer to starting your experiments. Get organized now! Start by gathering that pile of lab notebooks...your tasks on the go Never miss a deadline again. Organize you experiments, keep track of upcoming grant ... clippings, photographs, and file attachments. Organize your notes into notebooks, create checklists that...spreadsheets with lab members Now that you’ve organized your protocols, wouldn’t it be great if you could...reagent storage locations, such as the list used to organize your cryo freezer. No more issues deciphering ...

... model organism blog posts: Five Popular Model Organisms, Part 1 Five Popular Model Organisms, Part 2...diverse organisms. Methods for genetic manipulation still need to be developed for each organism, but researchers...and share all of these new organisms continues to be challenging. Organism specific viral vector systems...programs via Addgene. New organisms for genotype to phenotype studies New organismal systems described at ...and shared for many different organisms. Do you have a favorite organism you study in the lab? Let us ... work but never get to actually manipulate the organism they study (unless if you count normal human interaction...spiny purple sea urchin. It’s not a standard model organism, but it was easy to harvest eggs and sperm, mix...

...PMCID: PMC3531189. Mangone, Marco, et al. "UTRome. org: a platform for 3′ UTR biology in C. elegans." Nucleic...source project that is creating the “first virtual organism in a computer.” This project has produced various..., we have the entire SapTrap toolkit from the Jorgensen lab. SapTrap is a reagent toolkit and plasmid ...repair template of your choosing (Schwartz and Jorgensen, 2016). Using SapTrap, this CRISPR plasmid can...published in a microPublication (Schwartz and Jorgensen, 2018).  These are just some examples of worm ...PMC2238901. Schwartz, Matthew L., and Erik M. Jorgensen. "SapTrap, a toolkit for high-throughput CRISPR...Central PMCID: PMC4905529.  Schwartz, M. L., & Jorgensen, E. M. "SapTrap vectors for introducing point ...

...16), eadg6618. https://doi.org/10.1126/sciadv.adg6618 Stanton, A. C., Lagerborg, K. A., Tellez, L., Krunnfusz..., 31-50.e8. https://doi.org/10.1016/j.medj.2022.11.002 Tabebordbar, M., Lagerborg, K. A., Stanton, A.,...administration, distributing widely throughout the organism to target large or diffuse biological structures...specific application and animal model.  Other model organisms Tropism and efficacy can vary depending on species...target cell type or tissue of interest, and model organism under study. *Many engineered AAVs for mice use...Addgene Capsid Published Tropism Model Organism Mouse Strain-Specific Tropism?  Reference... and shows decreased transduction in off-target organs (Goertsen, Flytzanis, et al., 2022). AAV-PHP.N ...

...different organisms. There are several codons that encode the same amino acid. Each organism, however,...the genetic code is universal, many different organisms actually prefer certain codons over others for... biologist who wants to express genes from one organism in another? Let’s take a look at codon usage and...optimize codons for expression in a particular organism. Why is codon usage important? Translation and...for codon-usage of 257,468 genes across 8,792 organisms (Nakamura et al., 2000).  What is codon optimization...expression by changing synonymous codons based on an organism's codon bias. The idea is that scientists can make...mutations throughout a gene of interest based on an organisms codon usage bias to increase translational efficiency...

...across organisms. When using the MK system, many of the parts can be used in a variety of organisms, saving.... Crossref, https://doi.org/10.1038/s41598-019-46171-2. Resources on Addgene.org Modular Cloning (MoClo... these applications, no matter what your model organism is. MoClo background MoClo is a clever way to...MoClo kit recommendations for different modal organisms and applications.    Plant applications We...libraries and tools available for certain model organisms and backgrounds, MoClo can be invaluable for more... complex editing and screening experiments in organisms that don’t yet have these tools built out. While...many MoClo kits are designed with specific model organisms in mind, others are designed for flexibility. ...

...to mid-sized companies and organizations. Addgene as a nonprofit organization is very considerate and thoughtful... outside an organization The next step is to expand your efforts beyond your organization and/or scientific...people from various organizations in science and beyond. For example, I help organize scientific workshops...guide: Collaborating with others outside your organization also known as external collaborations. Interestingly...the ability to work with others outside one’s organization was found in the aforementioned survey as one... partnerships where we can leverage another organization’s expertise to our mutual benefit.  Our partnership...small: Collaboration opportunities within an organization but outside your comfort zone As part of my ...

...classification While CRISPR systems now seem neatly organized into their respective categories, arriving at ...CRISPR–Cas13. Nature, 550(7675), 280–284. https://doi.org/10.1038/nature24049 Altae-Tran, H., Kannan, S.,...terascale clustering. Science, 382(6673). https://doi.org/10.1126/science.adi1910 Chylinski, K., Makarova...Nucleic Acids Research, 42(10), 6091–6105. https://doi.org/10.1093/nar/gku241 Cong, L., Ran, F. A., Cox, D... systems. Science, 339(6121), 819–823. https://doi.org/10.1126/science.1231143 Cox, D. B. T., Gootenberg...-Cas13. Science, 358(6366), 1019–1027. https://doi.org/10.1126/science.aaq0180 Harrington, L. B., Burstein... enzymes. Science, 362(6416), 839–842. https://doi.org/10.1126/science.aav4294 Hu, C., Myers, M. T., Zhou...

...has taken place in other organisms. In many bacteria, unlike other organisms, CRISPR-induced double stranded...diseases have connections to either specific organisms or organism/gene interactions with the host. This scenario...can consider the microbiome as a collection of organisms, their genes, and metabolic processes, occupying...to diseases where the presence of just a single organism, such as Clostridium difficile, could be targeted... This approach successfully targeted specific organisms when using bacteriophages or mobile plasmids in...Pseudomonas species Expanding this tool to other organisms, the Ji lab brought genome and base editing to...genome engineering remains challenging for most organisms in the genus. Work from the Sun lab demonstrates...

... ease of use and utility in a wide variety of organisms.  While much of current CRISPR research focuses... plant species, including commonly used model organisms like Arabidopsis and Medicago truncatula and several...universal functionality of the CRISPR system in most organisms, some plant-specific changes to CRISPR components...experimental design principles developed in other model organisms (see our CRISPR guide for common CRISPR principles...sequence) is consistent between plants and other organisms, but the promoter used to drive gRNA expression...your gene of interest into a target cell line or organism (Presented in figure 1). More information on Agrobacterium-mediated...CRISPR/Cas system. Plant Methods 9:39 . https://doi.org/10.1186/1746-4811-9-39 Gao Q, Xu W, Yan T, Fang...

...to one or a subset of organisms. Examples: “organism agnostic”, “model organisms”, “small genome”, “large...require the organism to be specified and are truly organism agnostic. Other tools require an organism to be ...only one, or a subset of organisms. In only a few cases the software is organism agnostic. Most tools are...tools will be marked as organism agnostic and have currently available organisms listed in this section...input types can be readily converted.  Examples: “organism”, “sequence”, “identifier”, and “load”. Trends... tools also requiring that the user specify an organism. Output diversity: Different tools provide results...large genome”, and “organism biased scoring”. Trends: Many tools can handle genomes of any size and are...

...Therapy: An Overview. Cells, 12(5), 1–41. https://doi.org/10.3390/cells12050785 Murlidharan, G., Samulski...Frontiers in Molecular Neuroscience, 7. https://doi.org/10.3389/fnmol.2014.00076 References and Resources...the Mouse Brain. PLOS ONE, 8(9), e76310. https://doi.org/10.1371/journal.pone.0076310 Damdindorj, L., Karnan...adeno-associated viral vectors. PLoS ONE, 9(8), 1–10. https://doi.org/10.1371/journal.pone.0106472 de Backer, M. W. A...Hypothalamus. Human Gene Therapy, 21(6), 673–682. https://doi.org/10.1089/hum.2009.169 Dudek, A. M., Pillay, S., ... Receptor. Journal of Virology, 92(7). https://doi.org/10.1128/jvi.02213-17 Favre, D., Blouin, V., Provost...Journal of Virology, 76(22), 11605–11611. https://doi.org/10.1128/JVI.76.22.11605-11611.2002 Griffin, J. ...

...807, 141–157. https://doi.org/10.1007/978-1-61779-370-7_6 Tabebordbar, M., Lagerborg, K. A., Stanton, A....which allow AAVs to broadly spread throughout an organism, including difficult-to-target tissues like the...vector cargo designs and administration doses. Don't forget to submit your validation data after your experiment...the mouse brain. PloS One, 8(9), e76310. https://doi.org/10.1371/journal.pone.0076310 Bish, L. T., Morine...Human Gene Therapy, 19(12), 1359–1368. https://doi.org/10.1089/hum.2008.123 Dalkara, D., Byrne, L. C.,...Translational Medicine, 5(189), 189ra76. https://doi.org/10.1126/scitranslmed.3005708 Goertsen, D., Goeden...Methods & Clinical Development, 26, 331–342. https://doi.org/10.1016/j.omtm.2022.07.010 Issa, S. S., Shaimardanova...

... CRISPR-based genome editing in organoids By Ashley Waldron Organoids are three-dimensional cultures that...toolkit for performing genetics studies in organoids. The Organoid EasyTag System is a straightforward workflow...in an organoid model (Sun, et al. 2021).  Figure 1: Example schematic from the Organoid EasyTag...fetal-lung derived organoid system, the approach is intended to be amenable to organoids derived from other...find in this article: CRISPR-based editing in organoid Biosensors for detecting strigolactones The CRISPR... that mimic aspects of organ morphology and physiology in vitro and have emerged as a powerful model for...disease. In order to expand their model’s impact, organoid users have recently begun to develop CRISPR-based...