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When I started writing for the Addgene blog, I was focused on writing about new scientific techniques and cool plasmids. Creating graphics were usually the last thing I thought about when writing posts. Since then I’ve realized my figures are just as important, if not more important, than my writing. Initially I didn’t have access to professional-grade design software, like Adobe Illustrator, and I didn’t want to pay for these programs either. But with a little Googling and some trial and error, I found some free design software that let me create graphics that better communicated the science in my blog posts. This post highlights several of these free tools which will hopefully also help you communicate your science, whether it’s in presentations, manuscripts, or social media.

Direct reprogramming describes the process where differentiated cells are turned into a cell type of choice while bypassing the intermediate pluripotent state. Though a valuable tool for regenerative medicine, direct reprogramming is an inefficient process, with the majority of cells failing to develop the desired identity.

The development of single cell technologies, such as single cell RNA-seq (scRNA-seq), now allows scientists to identify the gene expression patterns unique to the few cells that successfully reprogram. Unfortunately scRNA-seq only captures the gene expression of cells at a single time point, making it difficult to investigate how early expression patterns influence reprogramming outcomes.

The vast majority of bacteria are undomesticated which limits the tools scientists can use to study them. For example, gene knockdown with CRISPR interference (CRISPRi) has been limited to lab-adapted bacteria because it has been challenging to introduce CRISPRi machinery into diverse bacteria species. Existing protocols can transfer CRISPRi into a single bacterial strain, such as a B. subtilis, or a narrow range of bacterial species, such as the human gut bacteria B. thetaiotaomicron, Mycobacterium, Pseudomonas, and E. coli. However, many non-model bacterial species lack genetic tools.

Mutagenesis is a tool that both evolution and molecular biologists use to tinker with DNA. Making changes to a DNA sequence can help scientists identify and/or facilitate the evolution of new phenotypes, and forward genetics harnesses this at a large scale by screening diverse libraries of genetic variants. Several methods for generating mutant libraries exist, but none provide a means to continuously diversify all nucleotides within a user-defined genomic region. EvolvR, a CRISPR-Cas9 based targeted mutagenesis method developed by the Dueber Lab at Berkeley, provides a new approach for generating novel genetic variants in bacteria. Read on to learn about the key components of EvolvR and its potential applications.

Autophagy (Greek for “self-eating”) is a process by which cytoplasmic material, including organelles, are targeted to lysosomes for degradation. Autophagy is a dynamic process which involves autophagosome synthesis, delivery of materials to be degraded to the lysosome, and degradation of autophagic substrates inside the lysosome. Historically, methods for studying autophagy focused on counting the number of autophagosomes. This approach, however, has inherent limitations because it turns a dynamic process into a static measurement and it provides limited information about what materials or organelles are being targeted for autophagy. The development of several fluorescent autophagy reporters now allows for the measurement of autophagic flux, or the changes in autophagic activity, and are a more reliable indicator of autophagic activity. The aim of this post is to provide an overview of four autophagy biosensors currently available from Addgene.