... FP binding domains forming a building block sufficient to seed polymer formation as fusion protein concentration...researchers remain unaware that EGFP/GFP is prone to forming noncovalent dimers. This property of EGFP can lead...GFP or another fluorescent protein (FP) could be forming dimers in cells. Why should you care? Three simple...prone to dimerization (i.e. EGFP) [1, 2] or even form obligate tetramers (i.e. DsRed) [3]. This is a problem...The propensity of a particular type of molecule to form a dimer depends on its molecular affinity, termed...high micromolar or low millimolar Kd is unlikely to form dimers in a cell. The Kd of EGFP is 0.11 mM [2]....outlined above, you might think EGFP is unlikely to form dimers in a cell. Unfortunately, things are not ...

...assembly, and possible solutions for each in the form of one-off scripts or programs, our goal was to ... new challenge: automating the bioinformatics steps needed to transform the raw sequencing data into a...building the entire ecosystem Proven performance with other bioinformatics purposes  Integrated user interface...DNA-based reagents. Not only do we extract as much information as possible from depositing laboratories and ... series, we will describe the importance of bioinformatics at Addgene and how our search for solutions...Labs.              DNA sequencing drives our bioinformatics needs       Fig. 1: QC'ing data at Addgene...was originally designed to help us work in large formats, such as 96-well microplates, and thanks to our...

... ready to transform when they begin flowering. It is important to perform the transformation not long ... dip transformation method. The general steps for this method include: Cloning and transforming a plasmid...obtain optimum transformation efficiency. It can take 6-8 weeks from the date of transformation to having ...2013). Preparing plants for transformation Whatever plants you are transforming into will be your T0 generation...pods), your plants may be too old to transform. This transformation could still work, but the efficiency... more chances to recover a transformant. Use young plants: If you transform early, your plants will still...plants per construct I transform. More seeds mean more chances to recover a transformant. Remove mature siliques...

...Last summer, we posted about our bioinformatics quest, which led us to Seqera Labs, a company that provides..., they break down the unique challenges of our platform and how we were able to address these issues using...

...announcing we have chosen to stop all activity on X, formerly Twitter. If you are interested in engaging with...LinkedIn. We are also exploring other social media platforms with active scientific communities and welcome...functionality and features that previously made the platform a mainstay of conversation in the scientific community...considering a gradual move off X as a response to major platform changes, such as limiting access and increased...

...through Informational Interviews. Making Your informational interviews productive Informational Interviews...connection? An Informational Interview is a great next step in your research. What an informational interview...interview is not If you ask for an Informational Interview it is understood to be a nonthreatening request ...before you need them (well really, always). Informational Interviews are for learning and for expanding...position at their company, do NOT call this an Informational Interview. If you do this, the connection may...does get easier with practice. Another perk of Informational Interviews is that it is a great way to practice...fields. My favorite final trick is to end each Informational Interview with the question, “Can you connect...

...when Amos Bairoch from the Swiss Institute of Bioinformatics reached out to us to tell us about a resource...resource called Cellosaurus, a growing cell line information database describing nearly 145,000 cell lines...dataset collections.  Depending on available information, entries may also include whether a cell line...lines may be especially vulnerable can be very informative. Spoiler alert: HeLa is the most common contaminator... fine grained query and retrieval of all the information in the resource.  This is a labor-intensive project...pdfs of the 26,000 publications cited. If the information seems incomplete or unclear, Bairoch follow up...are currently or planning to use for helpful information on the known features and relevant literature...

...mesothelioma that forms in the lining of the abdomen (peritoneum) – have the option of a new form of treatment...immunotherapy is coming to the fore as a cutting edge form of cancer treatment. With the goal of the Cancer...caused by exposure to asbestos, mesothelioma is a form of cancer that develops in the linings of certain...cause mesothelial cells to mutate and ultimately form cancerous tumors.  This process is not quick. It...susceptibility to developing mesothelioma, along with other forms of cancer. Additional research is being done to ...Greece. Current mesothelioma treatment As with many forms of cancer, the primary conventional treatments for...fight cancer. However, there are many different forms of immunotherapy that work in different ways. For...

...Traditional lab notebooks just won't cut it for bioinformatics. All kinds of biologists are finding themselves...prevent you from getting lost in the wide word of informatics. I am a molecular biologist who began coding ... one way to keep a virtual lab notebook for bioinformatics. In fact, there are endless ways and everyone...computation, but they will serve you well as you perform analysis after analysis after analysis… Treat ...background on other analyses that have inspired you to perform this analysis. Having a clearly stated, specific... each analysis will help you locate relevant information in the future. Approach: Outline a brief overview...the scripts and input files that will be used to perform each task. Conclusion: Always, always, write ...

...then form a blue precipitate. GUS is usually the first choice for establishing a new transformation protocol...that the transformation and gene expression can be tracked. During a transient leaf transformation, the engineered... we did our initial transformations with the GUS gene to see if the transformation was successful at all...before the transformation. We routinely transfer our plants 16 hours before the transformation into the ...can take even longer, a transient plant leaf transformation process could save the plant biologist some...pathway. Why plant scientists do transient leaf transformations The development of transgenic plants is a common... to years. In the plant sciences “transient transformation” usual means that neither a stable cell line...

...Aequorea victoria, AvGFP forms a homodimer. In corals, the red fluorescent proteins form tetramers. In general...proteins have a natural affinity and a tendency to form higher order aggregates. This property can be tolerated...The tendency of purified fluorescent proteins to form homodimers or higher order oligomers can be analyzed...meaning that at this concentration 50% of the protein forms dimers. Finally, spectroscopic methods (based on...or not FP-tubulin fusion proteins could properly form microtubule networks in cells. Other efforts tested...cells can be counted. This assay will provide information on the dimerization tendency in living cells....cell-type dependent. Therefore, it is good practice to perform this assay with your chosen FP in your cell type...

...microenvironments. These screens have primarily been performed in activated T cells, precluding analyses of T...cells. More broadly, this system can be used to perform in vivo screens in other cell types. A key feature...in vivo screens. Figure 1: Using FITS to perform in vivo CRISPR screens to assess T cell responses...

...transduction, and conjugation occur in nature as forms of HGT, but transfection is unique to the lab. Let’s take.... Eventually the cell lyses releasing the newly formed viral particles that can infect other bacteria....cells including transformation, transduction, conjugation, and transfection. Transformation, transduction...different methods of DNA insertion. Transformation Transformation is the uptake of genetic material from...environment. Various factors promote natural transformation in different bacteria such as growth phase ...increase cell membrane permeability and thus transformation efficiency. Check out Addgene’s blog to learn...our protocols page to learn about bacterial transformation in the lab. Gulp! Though bacteria don't...

...Fujii lab also developed another "in vitro" form. In this form, the CRISPR complex, consisting of a recombinant...additional information on CRISPR-mediated purification of a specific genomic region, other forms of enChIP.... These studies utilize a catalytically inactive form of Cas9 known as dCas9 (Jinek et al., 2012). Like...DNA-binding molecule (Hoshino and Fujii, 2009). Other forms of enChIP, that do not use dCas9, require Zinc-finger...Fujita et al., 2018). In addition to the "in cell" form of this method, in which an engineered DNA-binding... gRNA, were successfully used in this "in vitro" form. Any tag system can be used to isolate genomic regions...genomic loci through proteomics and the chromosome conformation capture (3C) technique. In addition to 3xFLAG...

...laboratory (BSL-3), a high-security facility needed to perform the experiments to demonstrate that this approach...humans. Then, one of them heard about our online platform, called Crowdfight, and filed a request for help...Crowdfight-COVID19 Crowdfight was born as a collaborative platform to help researchers working on COVID-19. Its origins...grew and became Crowdfight COVID-19, an online platform to connect researchers working on COVID-19 with... designers and other professionals, joined the platform; while they are a minority, their help has been... to push certain projects. The idea behind the platform was simple: any person working on COVID-19 could...and classified their responses, and used that information to deliver to the requesters what they needed...

...Associate Director of the Genetic Perturbation Platform at the Broad Institute, John Doench. A genetic... lightly. Whether executed in arrayed or pooled format there are of course materials costs, regardless...validity of your biological model and the technical performance of your assay. But, in many discovery-oriented...each with 4 gRNAs per kinase, so screens can be performed with either 4 or 8 gRNAs per gene. Further, the...the pools are available in two vector formats: all-in-one (lentiCRISPRv2, expressing both Cas9 and an ...genome-wide libraries, and thus can be screened in pooled format at a more-typical scale of tissue culture while...biological insight. Pooled and individual plasmid formats A first for a library at Addgene, you can also ...

...developing a moderate throughput functional genomic platform to annotate genetic perturbations that may play...activators” may be the direct drivers of tumor formation. Being able to parse out “neutral” passenger mutations...therapeutic interventions for cancer. This screening platform is an incredible boost to the cancer research ...

...of phage data and information. “We want to be the go-to place for phage information because there is so...so much information out there,” Zheng says. In the past year, they found that phage information was very...archiving information on individual phages. Integrating lab protocols, clinical information, phage research...clinicians. Creating a repository of phage data and information Since the inception of Phage Directory ~1 year...occurs. In addition to providing much needed information and potential for successful phage therapy, Sacher...

... the plasmid, and re-transform the ligated plasmid to recover the monomeric form of the plasmid. Have ...plasmid was observed to exist in various multimeric forms (e.g. concatemers, dimers, trimers, tetramers). ...in many different kinds of plasmids, taking many forms (Levene, 2009; Higgins & Vologodskii, 2016). Plasmid.... This recombination event produces a multimeric form of the plasmid with repeating sequences. In some...population as a mixture of monomers and various forms of multimers (Summers & Sharratt, 1984; Summers ... JR, Cooper DN, Bohr VA, Vasquez KM. Non-B DNA-forming sequences and WRN deficiency independently increase...Helinski DR. Characterization of multiple circular DNA forms of colicinogenic factor E-1 from Proteus mirabilis...

...tracrRNA is then mixed with recombinant Cas9 protein to form the ribonucleoprotein complex (csRNP, Figure 1).... scalability to the 96-well format, we developed a “TAG-IN” bioinformatics tool for guide RNA and donor...proteins interact with one another (or with DNA) to perform diverse biochemical tasks in the cell. One of the.../MS and ChIP-seq methods provide a wealth of information about how protein networks work in cells. A major...medium-throughput pipeline for epitope tagging. Using our 96-format pipeline, we can routinely achieve 5-30% tag knock-in...cost-effective and highly active. After csRNP complex formation, a single-stranded donor DNA (ssODN) that contains...experiments by assembling csRNPs in a 96-well plate format and tested parallel tag knock-in for 96 different...