...engineering pipelines, we selected Nextflow, a workflow management system for scientific pipelines, including... existed who had created a shared resource of pipelines for genomic data. Thanks to the flexibility inherent...separate Nextflow process. In Nextflow, a process defines which command or script will run and can be thought... connect each subsequent process to the existing ones. Once our first process was working as expected,...check, we repeated our strategy and copied a few lines of our existing script into the section of the next...

...in mouse embryos to generate gene modified mouse lines. Hopefully this post will help get your in vivo ...that later). Find Validated gRNAs to Target Mouse Genes To begin the in vitro screening process, you should... at the same time, and choose the most effective ones to increase your chances of gene modification in...a rapid acceleration in the production of mouse lines that could be used to study a wide variety of phenomena... et al. "Feasibility for a large scale mouse mutagenesis by injecting CRISPR/Cas plasmid into zygotes....generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering." Cell...

...Commercial Plasmid Prep Kit Amount 1000 Lanes 1000 Lanes 1000 Lanes Cost $200-$500  <$10 $20-30 Cost...commercial ladders cost between $200-$500 for 1000 lanes worth of ladder. The Penn State ladders are significantly...prep protocol, it cost less than $10 to make 1000 lanes worth of the 100 bp or the 1 kb ladder. Using a ...

...I really brought to the table was empathy, a willingness to listen, and an ability to remember the right...amount of conflict is actually critical in the business world. Companies and organizations that avoid ...involved, and also for the labs, organizations, or businesses as a whole. When I’m attempting to resolve a ... actively runs away from it. That can mean a willingness to make yourself temporarily uncomfortable for...while giving people the tools to resolve necessary ones on their own is even better. The Thomas Kilmann ...conflict resolution based on various levels of assertiveness and cooperation: avoiding, competing, accommodating...

...productive discussion first defines the material resources needed, then determines how much those resources...possible, this even includes clocks, timers, and phones.  As for reagents and consumables (such as pipet...time to decide what resources to keep, and which ones to abandon. It’s critical to make these decisions...1. First make decisions based on experimental timelines and specific aims. 2. Then make decisions based...productive and manageable laboratory environments. His business skills enhance his passion for science. Follow...

...526) that (1) enables efficient knockout (KO) of genes in immune cells; (2) is not immunogenic, a necessity... optimize conditions for a screen that assessed genes that regulate antigen-specific CD8+ T cell responses...screen, we used the pRDA_526 vector to knock out 30 genes putatively involved in CD8+ T cell responses to ... Ptpn2, Pdcd1, and Zc3h12a, demonstrating the robustness of the system and utility of the pRDA_526 vector...introduction of the model antigen, Ovalbumin, into cell lines to study antigen-specific responses. Find FITS plasmids...

...transcriptional effectors (LITEs) designed to bind specific genes and turn them on or off, literally at the flip of...are able to react and learn. All of this requires genes to be regulated dynamically.” To understand how ... tools to manipulate the expression of specific genes in the brain in reversible fashion. And that’s exactly... of living mice both quickly and significantly. Genes under LITE control showed a rise in transcription...researchers applied the LITE system to 28 different genes to establish it as “a novel mode of optogenetic ...

...focused on choosing a lab, but almost all of these guidelines can apply to any workplace or job. It amazes ...will need is about you. It’s worth taking time to honestly evaluate your own style of work and communication...below, the first question to ask yourself is “which ones matter to me?”  and hone in on the factors that ...Overwork – including undue pressure, impossible deadlines, unnecessary disruptions Destabilization – including...author order PI lets lab members fight it out PI intervenes if there are interpersonal conflicts PI has no...can be very helpful in uncovering strengths and weaknesses of the options. Use this blog as a guide. Start...

...and many plant scientists want to transfer large genes, smaller binary vectors with a larger cloning capacity...than that from the commonly used 35S promoter. Transgenes are also efficiently inherited in both transgenic...expression. Sahoo et al. have tested the system with genes up to 4 kb in length and confirmed successful protein... assays as well as stable expression of foreign genes in plants." PLoS one 9.6 (2014): e98988. Pubmed ...Plant Synthetic Biology Quick, Versatile Plant Transgenesis with GreenGate Plasmids Interview: Nicola Patron...

...dictator or laissez-faire; theory or practice; business-like or artistic; tech, anti-tech or pragmatic...employers love PhD students to have: working to deadlines, writing up clear and attractive reports, being...students and postdocs go on to work in patent law, business development, teaching, etc. Church also encourages...science and engineering (STEM) expertise in law, business, journalism, entertainment, politics, K-12, etc... passion, hard work, collaboration, and staying honest with personal goals. Stay tuned for the follow ...

...naturally occurring genes for cloning purposes (antibiotic resistance genes, toxin genes, and the sacB gene...gene of interest, but others will uptake plasmid backbones that re-ligated back on themselves. Therefore,...Plasmid cloning: Creativity with naturally occurring genes  At this point in the blog post, you may have realized...

...explosion SUperNova," SunTag can help you turn up the brightness in your fluorescent imaging experiments. Fluorescent...managed to track run lengths of the motor protein kinesin across microtubules. Tanenbaum et al. then tested...to traditional fluorescent proteins Improved brightness and signal-to-noise ratio Less chance of phototoxicity...used to improve CRISPR-based activation of target genes, but we’ll save that application for another day...on Addgene.org Find Fluorescent Protein Empy Backbones Visit Our Fluorescent Protein Guide Page Find ...

...both introduce genes into an organism’s genome (see figure) and to disrupt endogenous genes at the site ...by transposition assays of antibiotic-resistance genes conducted in HeLa cells). In their Nature Genetics... the rapid generation of stable transgenic cell lines which can robustly express your gene-of-interest...transposons rapidly generate stable transgenic cell lines. Biotechnol J. 2015 Feb 4. doi: 10.1002/biot.201400821...

...research project must have innovative yet attainable milestones that contribute to intellectual thought and discovery... and skills do you need to use to reach these milestones? Can you get assistance from people who have ...Think about what your personal goals are and set milestones along the way so that you don't get stuck doing...been developed. Can you think of a project that combines an exciting new method or approach with another... Passion fuels the drive to continue persuing milestones and working hard. Being patient, being selective...

...Now that we know all about antibiotic resistance genes, let’s consider another basic element of any plasmid...focused only on those found in bacteria. Some common ones you might see include ColE1, pMB1 (which comes in...20-40 CloDF13 (CDF) D Relaxed This table defines common cloning vectors, their copy number, ori,...copies of plasmids if they contain large inserts or genes that create a toxic product. The E. coli strain...for single- and multiple-unnatural amino acid mutagenesis in Escherichia coli. Biochemistry. 2013 Mar 12...

...validated simultaneously in the brain and the intestines of mice. The result? A very cool tool to advance...polymers are heated up and pulled to a desired thickness. The fibers are drawn with microelectronics included...engineering road map of sorts, giving an idea of the stiffness the fibers would need to be, as well as other ...fiber implants. Due to the soft nature of the intestines and the requirement for digestive motility to...excited a class of enteroendocrine cells within the intestines known as neuropods. They observed increased vagus...

.... Yet, we cannot prosper in a world where our medicines, technologies, defense, and governing policies...more scientists in our leadership, and raising awareness regarding the pitfalls of accepting alternative...chromosomes. Montreal, QC, Canada 45.5017°N 73.5673°W – Vanessa Sung Hundreds of scientists and supporters in ...well as allies outside the scientific community. Vanessa Sung is currently a PhD student studying breast...restorative justice.  Follow her on twitter @sung_vanessa. Albany, NY, USA 42.6526°N 73.7562°W – Nicholas...denying science, from celebrities falsely claiming vaccines cause autism to politicians saying that climate...

...mice Transgenic mouse lines have also been engineered to express various opsin genes [7-9]. The advantage...other tool in a scientist’s vast toolbox, its effectiveness depends on how and why it’s used. There are ...behavioral output is sufficient to assess the effectiveness of your optogenetic manipulations (though a ...has genetically manipulated a number of the opsin genes to alter the light spectrum for activation and the...advantage of using these lines is, if one is crossed with an appropriate mouse line expressing a particular ...

...Julio Ernesto Valdivia Silva, Universidad de Ingeniería y Tecnología (UTEC), Peru Julio Ernesto Valdivia...her current research, Sheen aims to identify new genes related to PZA-resistance by using different approaches...experience in the field of bacterial and fungal pathogenesis. Her research focuses on a collection of pathogenic...growth will then be measured to link the deleted genes to specific functions in biofilm formation. The...

...Cecchetelli Auxin Inducible Degradation (AID) uses plant hormones called auxins to conditionally and reversibly ...AID to yeast, as well as mammalian and human cell lines (Nishimura et al., 2009, Natsume et al., 2016).  ...protein of interest to create conditional human cell lines. Lastly, the Kanemaki lab demonstrated that auxinole...targeted by the Cas9 nuclease. The Streptococcus pyogenes Cas9 (SpCas9) requires an NGG PAM to recognize... role in the transcriptional regulation of many genes. A number of groups have designed means of studying...