...microscopic resolution for studying colloidal gold (1).  The method was based on using a thin plane (sheet...Siedentopf, and R,. Zsigmondy.  (1902) Ann. Phys.  315, 1 – 39.
 A. H. Voie, D. H. Burns, F. A. Spelman. (1993...microscopy/en_de/products/imaging-systems/lightsheet-z-1.html ...microscopy coupled with techniques that make tissues transparent are enabling microscopes to visualize the cellular...the cortico spinal tract, CST, spinal cord and cranial nerve afferents labelled with a AAV8 expressing...sectioning (OPFOS) (2). Arne Voie, David Burns and Francis Spelman focused a laser beam into a thin sheet ...of clear specimens and for in vivo imaging of transparent organisms. Advances in tissue clearing Similar...

...centrifugation (lenti) Centrifugation Titration time ~1 day (AAV); ~1 week (lenti) 2–10 days Initial titers Higher...will help you decide which is right for you. Table 1: Mammalian versus insect cells for viral production...only have to worry about cloning your transfer plasmid. The transfer plasmids have different packaging capacities...AAV and lentivirus requires three plasmids — a transfer plasmid containing your gene of interest plus ...in mammalian cells is relatively quick. After transfection, HEK-293T cells start producing virus within...systems, it is standard to do only one passage (transfection). This differs from typical insect cell preparations...an additional couple of days, as it requires transduction of more cells, while AAV can be titrated following...

...acceptable. Aims should be mechanistic, doable by 1-3 people in 1-5 years, and contribute to resolving the overarching...possible, do at least two full length practices (~1 h) and get feedback. It’s also helpful to practice...aims do not need to be grant aims. Each aim could be the basis of a single grant. Either way, think realistically...talk could be your plans for your first NIH R01 grant proposal or a 10-year research plan. I suggest preparing...is a significant need for healthy livers for transplants. Growth of new livers in culture could resolve..., neither of these can substitute for a liver transplant. My lab will combine bioengineered scaffolds ... for presenting a science talk Check out our transferable skills guide Read all of our career blog posts...

...experiments or even negatively impact cells (see Figure 1). When behaving properly, FPs enable researchers ... disulfide bonds in the secretory pathway (Figure 1) [4,6–8]. Additionally, FPs that encode N-glycosylation... sarcoma-associated herpesvirus.       References 1. Snapp, Erik. "Design and use of fluorescent fusion...excellent choice for fusions with integral membrane proteins and membrane associated proteins (i.e. GPI-anchored...these compartments undergo significant post-translational modifications including glycosylation, disulfide... addition of N-glycans [9]. Both of these posttranslational modifications can disrupt FP folding rendering...including the secretory pathway (Figure 2), the inner membrane space of mitochondria and chloroplasts, the extracellular...

...environments such as live cells and tissues (Figure 1). These flexible strategies give you the best of both...majority of in-cell labeling strategies have two parts: (1) a genetically encoded “tag” expressed as a fusion...Follow him on twitter @rhodamine110.   References 1. Liu, Zhe, Luke D. Lavis, and Eric Betzig. "Imaging...requires more photons. For example, moving from transient overexpression of protein fusions to gene-edited... lipoic acid ligase, biotin ligase, phosphopantetheinyltransferase) – These enzymes catalyze the covalent... tag (Figure 1c). Click chemistry (e.g., transcyclooctene–tetrazine)– Nonnatural amino acids can be ...improved brightness, photostability, and spectral range. Nevertheless, these fluorophores were designed ...

...a rate of up to 1 per 500-1000 bp. In comparison, the DNA replication error rate is 1 per 109 bp. Unlike... and Screening via Transcriptional Output-TANGO (PRESTO-TANGO) to screen the NCC-1 library of approved...(MAGE) (1). MAGE uses recombineering (2) to simultaneously incorporate multiple single-strand DNA (ssDNA...generated 5 common 30bp overlap sequences (Sites #1-5). Each overlap site encodes a unique restriction...First, GMAP-compatible backbones for lentivirus LV 1-5 and retrovirus RV 2-5 were constructed. The authors...of GFP (SEP) by a 9 amino-acid linker (see Figure 1). The key to the biosensor lies in pH: DsRed is relatively...inactivate SEP and leave only DsRed to fluoresce (1). With variants that can be targeted to specific cellular...

.... pH and DNases affect DNA stability Figure 1: So many choices! What to do? The main factors ...your downstream experiment. TE (10 mM Tris-HCl,1 mM EDTA, pH 8.0) buffer is the best buffer for preserving...from the DNA. These apurinic sites if in double stranded DNA are repaired by base excision repair, but ...but can lead to mutations in single stranded DNA undergoing replication.   DNase on the other hand can digest...

...’re not one of these people yourself.  Fig 1: Quote from Michael Ende, courtesy of morefamousquotes.com... blog Management for ScientistsTransferable Skills Guide: LeadershipTransferable Skills Guide: Teamwork...the right time. Like many of the posts in our Transferable Skills series, this post is not meant to be ... that you could strengthen. The right set of transferable skills, coupled with your technical skills, ... can help, and if and when you find yourself transferring this skill to another job, it will be important...also aggravate long-term personal conflicts.  Transitioning a conflict into a collaboration may not be the...willing and able to solve, don’t take that skill for granted. When you go on interviews or are looking for a...

...my master’s, I worked in an academic lab where I ran a handful of assays over and over. Everyday was the...help you decide if a master’s might be for you. 1. Are you interested in master’s-level jobs? Ultimately...your work at conferences, help with manuscript and grant preparation, and lead your own research project....

... Figure 1: With blue light, the VVD domains of the BLADE dimerize and activates transcription. The ... that dimerizes upon exposure to blue light (Fig. 1). Another blue light-inducible dimerization domain...from one that represses transcription to one that activates transcription.However, this system lacks spatio-temporal...barbara_synbio) May 13, 2021 The original AraC transcriptional regulator Their system is based on the AraC...AraC protein that controls transcription from the PBAD promoter. “AraC is widely used in synthetic biology...It relies on the sugar arabinose to activate transcription by causing conformation changes in the AraC ...your gene of interest, all you have to do is co-transform pBLADEONLY. That way, a previously cloned gene...

... genetic tools in Drosophila (Fig. 1):  GAL4-UAS, a transcription factor binding site. GAL4 expressed...Rodríguez et al., 2011).  Genetics of SPARC Figure 1: SPARC and SPARC2 use the GAL4-UAS system along with...visualize individual/non-overlapping cells. While transgenic animals are commonly used to specifically manipulate... to trigger recombination and expression of a transgene (Lin et al., 2018). However, this system requires...site to cleave and inactivate any read-through transcripts of the effector gene. Effector genes, any gene...across cell types and organisms by replacing the transcription factor binding site and effector in the construct... the SPARC system to use other experimental transcription activation systems, such as LexA/p65 or mCD8...

...our lives. Plasmid transformation into E. coli is a fairly inefficient process– just 1 out of 10,000 cells...down especially fast and plates should be used witin 1 month for optimal efficiency. Beware of satellite ...aminoglycoside Binds 30S ribosomal subunit; causes mis-translation Bactericidal 50-100 ug/mL Spectinomycin aminoglycoside...Blocks 50S ribosomal subunit; inhibits aminoacyl translocation Bacteriostatic 50-100 ug/mL in EtOH Polymyxin...Polymyxin B polypeptide Alters outer membrane permeability Bactericidal 10-100 ug/mL Tetracycline tetracyclin...Binds 50S ribosomal subunit; inhibits peptidyl translocation Bacteriostatic 5-25 ug/mL in EtOH *In prokaryotes...

...B. Gurumurthy, and Masato Ohtsuka. Nat Protoc. 13(1) (2018):195-215. PubMed PMID: 29266098 Creating knock-in..., with protocols using dsDNA templates achieving ~1-10% efficiency. Easi-CRISPR uses a long ssDNA template...sub-pathways like synthesis-dependent strand annealing (SDSA) and single-strand DNA incorporation (ssDI). "Easi-CRISPR...These complementary goals are aimed at improving translation of CRISPR technology, but they would also bring...a DNA repair newbie - diagrams of resection and strand invasion are like a foreign language to me. But...supports over 250 genomes, and they just released a brand new CRISPOR manual to kick off 2018! "Mechanisms...

... similar antibodies in llamas and alpacas (Figure 1). At the time, researchers were already on a quest...nanobodies (Arbabi-Ghahroudi, 2017)!      Figure 1: Comparison of a heavy-chain only antibody and single-domain... tools for diverse applications. For example, RANbodies can be used as an alternative to conventional ...sdAbs were used to create GFP scaffolds for transcriptional activation.  sdAbs in the clinic sdAbs have...also been some interesting work done developing transgenic mice that express camelid variable domains (aka...Llamas Required - Synthetic Nanobodies Against Membrane Proteins More resources from addgene.org  Plasmids...

...organoid model (Sun, et al. 2021).  Figure 1: Example schematic from the Organoid EasyTag system...without altering that of the internal control (Fig 1). Because this method relies on the fluorescence ratio...B) Strategy for leak-free transcriptional control. C) Iterative transduction workflow overview. Image ... by integrating a SL-insensitive fluorophore (LSSmOrange) as an internal control and a SL-sensitive fluorophore...fluorescent biosensor has a high sensitivity (50 nM-500nM range) and a high specificity for SLs in vitro, and they...

...more tools for plasmid mapping and design (Figure 1). Benchling: While you might think of Benchling as...Davis from the University of Utah.   Figure 1: A plasmid map created in SnapGene of Blue Flame plasmid...sequences to sequences in a database ExPASy translation tool: Translates a DNA sequence using all six open reading...Annotates features, BLASTs, aligns, digests, and translates a sequence.   NEBCutter2: For finding restriction...information, such as expression patterns, post-translational modifications and polymorphisms Codon optimization...

...cleavage. NgAgo takes a different approach, randomly removing 1-20 nucleotides from the cleavage site specified...About NgAgo User's First Impressions Here References 1. Gao, Feng, Xiao Z. Shen, Feng Jiang, Yongqiang Wu...in the cell. gDNA guides will also need to be transfected into the cells of interest. In contrast, RNA ...must be expressed from a plasmid or in vitro transcribed, and changes in gRNA secondary structure can ...removal RNA-guided CRISPR enzymes cause double-stranded breaks, with either blunt (Cas9) or staggered ...

...from distantly related organisms. In 2006, less than 1% of the genes deposited at Addgene were synthetic....synthetic biology is expanding rapidly.  References 1. Kunjapur, Aditya M., Philipp Pfingstag, and Neil ... synthesis companies often work within a narrow range for GC content. Rare codons also are not good predictors...sequences is Proteobacteria - the most frequent transfer of genes is from Proteobacteria to mammalian expression...natural gene sequence is, the less likely it is transferred into another organism in the lab. Predicting ...

...optimized for expression in E. coli: acoustic gene 1 (arg1) and acoustic gene 2 (arg2). The key difference... plasmids are available from Addgene! References 1 Bourdeau, R.W., Lee-Gosselin, A., Lakshmanan, A., ...expressing ECN is 109 cells/ml, which is within the range of  the ~1011 commensal bacteria per gram of stool...

...this system.  Fig. 1: Cytidine deamination takes place on the free strand of DNA and converts a C...guide RNA (sgRNA), provided it meets two conditions:  1) The sequence is unique compared to the rest of the...temperature-controlled genome editing. Nat. Commun. 2017 81 8, 1–9 (2017).Walton, R. T., Christie, K. A., Whittaker...changing its double-strand cut to a single-stranded nick. In order to produce a double stranded break, two sgRNAs... target DNA. The reverse transcriptase polymerizes DNA onto the target strand based on the sequence of...targeting dCas9 to transcriptional start sites was sufficient to repress transcription by blocking its initiation...approach is that two sgRNAs targeting opposite strands must be available in moderate proximity to each...