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TypeBlog PostPublishedJuly 17, 2018, 12:23 p.m.... hands-on, it will be “brains-on”! I know that even lectures should be “brains-on”, but as much as I try...received a whole set of cards (Promoters, Inserts, Tags, Origins of Replication, Resistance gene and Selection...
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DAP arrays for multiplex gene editing
TypeBlog PostPublishedJuly 7, 2022, 1:15 p.m....organisms. However, lengthy genetic payloads and insufficient transcription on the array have limited the ...editing. How do you then set up an MBE system that contains a double-win for both efficiency and multiplexity...lentivirus, demonstrating simultaneous editing of genes against multiple genetic diseases, such as muscular dystrophies...CRISPR-based gene editors, for correcting mutations or installing functional genes to study and potentially treat... -
Plasmids 101: Mammalian Vectors
TypeBlog PostPublishedMarch 25, 2014, 3:15 p.m....and are not used for general plasmid selection. Instead, reporter genes are often employed to easily monitor...of picking up positive traits (i.e. the plasmid contains a cassette that will make cells resistant to a...picking up of a negative trait (i.e. the plasmid contains a cassette that will make cells sensitive to a... should not be used for mammalian expression – instead use G418. This can be confusing since the neo/kan... -
Cancer, Inflammation and Immunity - Harnessing the Body’s Defenses to Fight Cancer
TypeBlog PostPublishedJuly 6, 2017, 1:59 p.m....immune system to fight progressing cancers. It was inspiring to participate in the 2017 Cell Symposium on Cancer...presentation by Professor Guido Kroemer from the Institut Gustave Roussy. Professor Kroemer discussed the...Professor Caetano Reis e Sousa from the Francis Crick Institute concluded “Aspirin promotes autophagy, inhibits...session I got a chance to talk with Dr. Friedmann-Morvinski about tools used to analyse the tumor microenvironment... -
Improved Plasmid Maps Powered by SnapGene
TypeBlog PostPublishedJune 29, 2017, 1:06 p.m....resistance genes, selectable markers, promoters, origins, tags, and certain ORFs. Their sophisticated detection...only a few nucleotides, such as the fluorescent proteins EGFP and mEGFP. Many of these features, such as...Map” and “Sequence” tabs. Primers This tab contains a table listing commonly used primers detected...Additionally, align a custom nucleotide sequence against a given sequence using BLAST2. See this blog post... -
Flow Cytometry Readouts: Yes, No, and Everything in Between
TypeBlog PostPublishedAug. 20, 2024, 1:15 p.m....looking to study the level of protein expression, instead of its presence or absence, the plots can look ...These smears tend to occur when you are looking at proteins that are expressed regularly in cells and might...Created with biorender.com. In such cases, instead of trying to quantify based on percentage positive...with normal gates, just based on a histogram plot instead of a dot plot. However, the histogram plots look... -
CRISPR 101: Non-Homologous End Joining
TypeBlog PostPublishedApril 16, 2015, 3:45 p.m....) if NHEJ joins the distal ends together. Similarly, it may be possible to direct insertion of an exogenous...of breaks) by NHEJ-dependent repair (“pop-in” insertion) provided a template containing compatible overhangs...Renouf B, Renaud J-B, Sallmyr A, Ruis B, Oh S, Tomkinson AE, Hendrickson EA, Giovannangeli C, Jasin M, ... -
Advice for Starting a Biotech Company from a Grad Student turned Entrepreneur
TypeBlog PostPublishedJuly 10, 2014, 7:17 p.m....healthcare settings, etc. What project in the Collins lab inspired Sample6? The initial work focused on using..., and the team that packages its pitch the best, wins. He explained that entrepreneurs must clearly communicate...failure at all stages in the startup". To gain insight into "the random-walk" of a budding startup, I ... -
Stabilized Bacterial Promoters: Constant Gene Expression at any Copy Number
TypeBlog PostPublishedSept. 4, 2018, 12:53 p.m....3-100 per cell, a stabilized promoter buffered against the effects of copy number on reporter gene expression...promoters drove maximal gene expression near genomic origins of replication, the stabilized promoters created...deoxychromoviridans requires three genes whose proteins are needed sequentially. When Segall-Shapiro et...optimization of gene dosage in E. coli using DIAL strains." Journal of biological engineering 5.1 (2011):... -
It’s Bioelectric! An Exciting Interdisciplinary Field of Research
TypeBlog PostPublishedOct. 29, 2019, 2:52 p.m.... the imbalance of electrical charge between the inside and the outside of the cell. This imbalance is ... Examples of some genes encoding gap junction proteins cx43 GJB1 GJB2 Bioelectric states can alter ... even between many cells (through gap junction proteins which connect the cytoplasm of two cells) can ...controlled by the opening and closing of ion channel proteins, they are not always easy to track at the transcriptional... -
Antibodies 101: Conjugation
TypeBlog PostPublishedMarch 26, 2024, 1:15 p.m....make sure that they’ll be compatible with your instruments, each other, and your target. I love FPbase’s...reaction, can be detected using specialized imaging instruments or X-ray film and lends itself well to assays...mechanisms. Most take advantage of chemical groups intrinsically present on antibodies, such as the primary amine...that make up the disulfide bonds between antibody chains. 3) Endogenous carbohydrates added to antibodies... -
The Future of Research Symposium Boston 2015
TypeBlog PostPublishedOct. 20, 2015, 2:30 p.m.... to train our young scientists for futures both inside and outside of academic research (4). There are...industry, regulatory, or clinical environment. It remains contested, however, whether a better solution would...University, has recently published an article arguing against reducing the number of graduate students accepted...grassroots organisations that represent postdocs and institutes that employ them, the diversity of trainee backgrounds... -
Writing Scientific Manuscripts: Literature Searching, Reading, & Organizing
TypeBlog PostPublishedMay 5, 2015, 3:54 p.m....though you may need to be on a network with an institutional subscription), archived on PubMed Central, or...Check out the hashtag #365papers on Twitter for inspiration and accountability. There are a few different...reprints and papers with scribbled notations in the margins. If you prefer, printing and hand-writing notes...guest blogger! Johnna Roose is a biochemistry instructor in the Department of Biological Sciences at Louisiana... -
Plasmids 101: Cre-lox
TypeBlog PostPublishedJan. 13, 2015, 3:47 p.m....number of important plasmid elements – promoters, origins of replication, protein tags, and antibiotic resistance... Cre acts independently of any other accessory proteins or co-factors, thus allowing for broad applications...no chance of it occurring randomly. Therefore, inserting loxP sites at deliberate locations in a DNA sequence... a parallel orientation, allowing the four Cre proteins to form a tetramer. A double-strand DNA break ... -
Overcoming the Challenges of Lentiviral Production
TypeBlog PostPublishedAug. 7, 2018, 12:31 p.m....high titer virus for transfer plasmids with small inserts (such as CRISPR guides) while a single 72h harvest... This is due to inefficient packaging of large inserts; a study by Kumar et al. found that in some cases...titers can drop 10-fold for every 2kb increase in insert size. To overcome this, lentivirus can be concentrated...require an ultracentrifuge, PEG will precipitate all proteins in a solution, not just the lentivirus; consequently... -
Corralling and Cornering the Goldilocks Antibody
TypeBlog PostPublishedAug. 9, 2022, 1:15 p.m....unreliability: cross-reactivity (binds to non-target proteins), variability (separate batches can perform differently...mostly uses whole-mount IHC techniques on rodent brains and is expanding to more complex brain systems ...larger-volume antibodies for thicker tissues and whole brains, we chose monoclonal antibodies (mAbs) and their...negative control which does not have primary and only contains secondary antibodies, allowing us to only image... -
Design Tips for Prime Editing
TypeBlog PostPublishedJan. 23, 2025, 2:15 p.m....). Figure 3: pegRNAs whose 3′ extension begins with a C base can cause unwanted base pairing (...BioRender.com. What to edit The sequence you choose to install can influence the success of your prime edit. If...sgRNA is designed to bind only after the edit is installed. This reduces concurrent nicks, which lowers indel...so that nicking only occurs after the edit is installed on the opposite strand. Created with BioRender.com... -
Viral Vectors 101: Calcium Sensors
TypeBlog PostPublishedAug. 10, 2023, 1 p.m....indicators (GECIs) are fluorescent proteins linked to calcium binding proteins (e.g., calmodulin or troponin... changes with Ca while another wavelength is insensitive. Additional red sensors based on mRuby (jRCaMP1...Addgene.org Addgene’s AAV Guide Fluorescent Proteins: Biosensors Addgene’s Viral Services Resources... -
Adeno Associated Virus (AAV) for Cell and Gene Therapy
TypeBlog PostPublishedNov. 7, 2017, 1:59 p.m....that treat disease at the molecular level. For instance, if a disease is caused by a mutation in a single...deficiency, Cystic fibrosis, Muscular Dystrophy, Parkinson’s disease, and HIV. A notable landmark study showed...showed significant clinical efficacy against a form of blindness known as Leber’s congenital amurosis ...example, prevalence of neutralizing antibodies against some AAV types, AAV1, 2, 3 and 5 are thought to... -
6 Tips for Grant Writing
TypeBlog PostPublishedOct. 18, 2016, 2:30 p.m....in different fields that can provide different insight into an area - not just working within the established...of expertise, equipment, or excellence of the institution). Likewise, if you’re staying in the same lab... applying for smaller grants from within your institute or a private funding body. Success breeds success...collaborators can also help you get some critical insight into what you're doing wrong. All this helps to...