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...everyone at this specific conference, and I was able to include and exclude different modules for this workshop...something about it. Building a diverse team with different talents and expertise Fortunately, the eLife ambassadors...realized that holding the next one at a scientific conference could potentially enable reproducibility practices...it physically to instruct the workshop at the conference, but because each contributor made the materials...open and modular nature of the workshop content: different parts could be mixed and matched to serve a specific...the lookout for upcoming workshops at future conferences this year. Workshops are confirmed for the Evolution... having a workshop organized at your upcoming conference or you’d like to join or contribute to this collaboration...

...reads are mapped against a reference sequence, if one was provided. If no reference is given, de novo assembly...functioning properly or be something completely different than what was originally intended. Sharing unverified...scientists worldwide. Depositing scientists provide different types of data for each of their plasmids, from...plasmid sequence de novo (without the use of a reference sequence) using a bioinformatics pipeline developed...scientists to easily visualize and identify sequence differences between our NGS results and deposited sequences...mismatches in significant plasmid elements. Which differences are considered a QC issue is reviewed yearly ...approaches to confirm plasmid sequences without a reference; and identifying mixed plasmid and nucleotide ...

... Types of ELISA There are four different types of ELISAs, which differ in the way the antigen is detected... to run an ELISA in your lab!   References and resources References Boguszewska, K., Szewczuk, M., Urbaniak...Antibodies are used in many different experiments that require scientists to detect proteins in their...antibody and the detection antibody recognize different epitopes on the target protein, so they do not... for which multiple antibodies that recognize different epitopes are available; this type of ELISA is ... are coated with another protein — known as a reference antigen — that can also bind to that antibody....antigen as the other types of ELISAs require two different antibodies. As mentioned above, it can also be...

...section, teams are assigned different groups of three genes selected from different parts of the Met pathway...first select a multi-gene pathway to study and a reference organism where deletion strains are available....Students next transform deletion strains from the reference organisms with the overexpression plasmids. Finally...species has a similar function to the gene in the reference species. We have been using yeast models (3, 4...yeast, Saccharomyces. cerevisiae, makes a great reference organism for the project because it is non-pathogenic.... Over time, the two genomes have become very different due to a whole genome duplication and extensive...cloning to insert the coding sequences for ten different MET/Met genes (Figure 1) from the two yeast species...

...drawbacks of different methods (for comprehensive protocols for all of the methods discussed here refer to Kutner...the correct transfer plasmid was used in the transfection; if preparing several different lentiviruses...assaying for expression of a gene carried on the transfer plasmid or quantifying the number of viral copies...resistance-genes, or the transgene itself. Many researchers prefer to design primers that target the common features...utilizes the antibiotic resistance genes carried on transfer plasmids. Target cells are transduced with serial...that standard conditions be used when comparing different batches of virus. In addition, some viral preps...step of a successful transduction experiment. References 1. Kutner, Robert H., Xian-Yang Zhang, and Jakob...

...to learn how to adapt to different situations and, in particular, to different styles of leadership. As... one gain such experience? Your institution may offer occasional workshops on leadership and management...to learn more. Having met many people at that conference, I later became involved with the NPA beyond ... the Committee which I then led for 5 years.  Different leadership styles Being an effective leader requires...requires you to understand how to work with many different types of people both above and below you. During...relationships with these individuals who often had different styles from their predecessors. Changes were implemented...mission of the NPA. You must accommodate many different types of people in order to harness their strengths...

... in mice Many systemic capsids express differently in different mouse strains, a phenomenon that we are...And these differences occur not just between mice and NHPs; some capsids show both different efficacy ... systemic capsids. After some consideration, we offer this definition: A systemic capsid is a capsid that...Organism Mouse Strain-Specific Tropism?  Reference AAV-PHP.B* CNS (broad) Mice, rats Yes...sex-independent and does not show significant differences in transduction efficiency between C57BL/6J and...transduction efficiency varying from 10-70% in different regions of the brain (Ravindra Kumar et al., 2020.../cJ and CBA/J mice. AAV1-X1 was developed by transferring the 7-mer peptide region from variable region...

...discomfort of the mice, and restraint method. Many different substances can be injected, including cells, drugs...through the tail vein — many researchers will simply refer to these as “tail vein injections.” However, they.... They are a popular choice for administering different drugs and viral vectors. Like IV injections, intraperitoneal...flat, and easily accessible (like the back) is preferred. A common use of intradermal injections is studying...techniques may come in handy. These techniques are referred to as “instillation” or “gavage,” as they do not...as both procedures target the lungs. The main differences are that intranasal is easier, less invasive,...be flexible or metal, depending on researcher preferences. It sounds complicated but has a pretty low learning...

...overlapping markers. Compensation/reference control(s) Compensation or “reference” controls are samples stained...spectral flow cytometry are more alike than they are different, there are a few aspects in which spectral flow...complex mathematical algorithm and single stained reference controls to distinguish one fluorophore from another...   Figure 3: Similarity index across 12 different colors on a three laser spectral flow cytometer...conventional or spectral flow. In spectral flow, reference controls tell the software to look for that exact...is not the same as your single color control. Reference controls: Beads or cells? Compensation beads are...new panel on a spectral cytometer, you prepare reference controls of both beads and cells for a single ...

... of the plasmids in our repository with known reference sequences, such as full plasmid sequences provided...BLAST, which includes a simple explanation of the different BLAST programs, databases, and elements of the...The blastp and blastx programs are optimized differently and you may want to select one (or both) depending...you want to verify. We will delve into these differences below. Optimizing blastn searches On the Standard... a Sanger sequencing result to a single known reference sequence or to a BLAST sequence database. If you...two or more sequences” checkbox and paste your reference sequence into the Subject Sequence box that appears...BLAST searches. If you do not know the exact reference sequence for your result, choose one of the BLAST...

...exact location of the TSS. Different databases annotate the TSS in different ways, and it has been shown...phenotype of interest. This blog post will discuss differences between these approaches, and provide updates...Doench et al., 2017, and Hanna et al., 2020) and references therein.   {% module_block module "widget_fcf9eab0...are so few gRNAs to choose from that sequence preferences must largely be ignored. Created with ...few potential gRNAs. While SpCas9, with a PAM preference of NGG, is still the most widely-used Cas enzyme...Cas12a enzymes, and engineered variants thereof offers additional PAM options that can greatly expand ... with BioRender.com. Two newer technologies offer an alternative to HDR for introducing edits. The...

... that differences in gene expression could explain why some ancestry groups were differentially dependent...ancestry-associated genes.   What does the reference genome actually reference?  The CRISPR guides used in the screens...done in this preprint.   Resources and references References Germline variation contributes to false... were designed to have a perfect match to the reference genome – even single mismatches within a CRISPR...introduce significant bias into the results. But the reference genome does not represent the diversity of genetic...understand how the use of a primarily European reference genome could affect their analysis. Their work...these and any other CRISPR screens using the same reference genomes and libraries. Further complicating the...

...Addgene blog Plasmid Preps: Different Purity, Different Quantities, Different Uses What's the Best Way to... our blog and website.          References and Resources References Ahlfen SV, Schlumpberger M. Effects...Each of these contaminants will have a slightly different impact on the spectra of a mixed sample.  ...A260/230 of ~2.0. However, let’s break down how different contaminants impact these ratios.  Protein contaminants...significantly at low concentrations.  The elution buffer you use will also affect how accurate your measurements...give more variable absorbance readings. A Tris-buffered solution tends to produce more consistent readings... instrument you use and check out some of the references we have provided below. And if you do have trouble...

... the split-luciferase system, intein-mediated splicing reconstitutes functional luciferase only when fusions...when separated (2), and that DBD and TAs from different systems could be combined effectively (3). In ...target gene, in this case a reporter gene (e.g. luciferase or GFP), regardless of whether it interacts with...sequence of the DBD. The DBD-POI fusion (commonly referred to as the “bait”, Figure 2b) cannot activate reporter...interact, this will bring the POI-TA fusion (commonly referred to as the “prey”) in close enough proximity to... fusions of the two halves of the luciferase protein interact and enable intein splicing (5). Screening...a more vigourous screen is to use a number of different bait and prey vectors. This has been shown to ...

...experiments. The term ‘insert’ refers to plasmids carrying each part, ‘vector’ refers to acceptor plasmids, and...MoClo guide for all the basics of the process. Also refer to Figure 1 for a visual overview! Figure...vectors and parts you will be using during the different levels of your MoClo assembly. Know your process...dictated by four-base overhangs that are paired with different part types (e.g. 5’-GGAG and 3’-TACT flanking ...ensure that these would be interchangeable between different laboratories. Therefore, choosing acceptor vectors... Example Level 1 assembly. The choice between different Level 0 vectors depends on the four-base overhangs...MoClo plate, always do so in cold conditions and preferably on dry ice. Careful use of your glycerol stocks...

...protects against any of them. But different aminoglycosides work on different host species: kanamycin targets... unrelated host species, even from completely different kingdoms of life. That’s convenient for researchers...experiments in complex eukaryotic cells, but would prefer to grow, clone, and manipulate their vectors in...with BioRender.com. How are shuttle vectors different from other plasmids? If we all use the same molecular... Shuttle vectors have to address several big differences in the ways vectors are used across species: ...resistance gene on your vector might require two different selection molecules! It all depends on how the...Auxotrophic selection Another option is to use a different method of selection entirely. Auxotrophic selection...

... of the vectors in Addgene’s catalog are offered in different serotypes. In fact, the 879 viral vectors...these tools can be to use. AAVs, which can target different cell types depending on their serotype, are particularly...to researchers around the world. While we still offer many resources for producing vectors from plasmids...93,491 viral vector preps with researchers in 45 different countries — and as of 2024, we’ve distributed ... CRISPR, where we dove fairly deeply into the different types of tools scientists were using/depositing...prioritization happens for good reasons. We began offering our viral vector service because we realized that...successive generations developed ever since. GCaMP6 was offered through our viral vector service in 2016, and it...

...virus:  Lowering cytotoxicity. Different envelope proteins have different levels of cytotoxicity and the...Altering sensitivity to serum. Different pseudotyped viruses are differentially inactivated by nonspecific...Table 1 (Cronin et al., 2005)     References and Resources References: Crawford KHD, Eguia R, Dingens AS...protocol for generating lentivirus, but you use a different envelope glycoprotein instead of the wild-type...Lentiviral production uses three plasmids: (1) The transfer plasmid, (2) the envelope plasmid, and (3) the...review articles to find tables and information on different viral membranes, tropism, and advantages and disadvantages... Jennifer Tsang...

...more stable than the methyltransferase. When a plasmid is lost, the methyltransferase is degraded and/or...of CcdB (toxin) and CcdA (antitoxin) where CcdB inferes with DNA replication by binding the GyrA subunit...composed of restriction endonucleases and methyltransferases. Restriction endonucleases cleave DNA at ...specific nucleotide sequences. To counter this, methyltransferases add methyl groups to bases at specific nucleotide...address a diverse set of biological inquiries. References Ogura, Teru, and Sota Hiraga. "Mini-F plasmid...genes that couple host cell division to plasmid proliferation." Proceedings of the National Academy of Sciences...Cara E., and James B. Kaper. "Use of stabilized luciferase-expressing plasmids to examine in vivo-induced...

...gene which differ between the AAV serotypes are responsible for serotype-specific differences in tissue...blog post to learn more about the AAV transfer plasmid! References: Naso MF, Tomkowicz B, Perry WL III...proteins needed for the virus to replicate,  and the transfer plasmid which contains the viral genome. In today... proteins. Alternative splicing generates the different C-terminal regions of the Rep proteins. While ...Replication initiates from the AAV genome ITRs on the transfer plasmid, which contain regions of dsDNA. To generate...the AAV p40 promoter. Alternative splicing and differing translational start sites generate the three VP...was engineered Learn about the parts of the AAV transfer plasmid  Resources on Addgene.org Learn about...