... a more-typical scale of tissue culture while still offering the potential for true biological insight...which to test the validity of your biological model and the technical performance of your assay. But, in...components, the model system and the assay are just as critical for success. Sometimes, you might have a few positive...involved. Or you don’t know how well your assay will scale. Or you don’t have enough cells to execute genome-wide...facilitating more rapid follow-up. We hope the biological community will find these reagents to be useful...

... that could bind very specifically to target molecules. Using a technique called systematic evolution ... high specificity and affinity, were eventually called aptamers, from the Latin aptus, meaning “to fit...essentially mimicking GFP.  Though the aptamer, called Spinach, required longer exposure time than its...group selected for a 49-nucleotide aptamer they called Broccoli. As a product of SELEX and FACS, Broccoli..., Akhtar and Marty, Jean L. “Aptamer based electrochemical sensors for emerging environmental pollutants...PMCID: PMC4923196. 8. Sassolas, Audrey, et al. “Optical detection systems using immobilized aptamers.” ...9. Song, Kyung-Mi, et al. “Aptamers and Their Biological Applications.” Sensors (Basel). 2012; 12(1): ...

...institutions set their postdoctoral salary scales to the NRSA scale (Figure 21, National Postdoctoral Association...addition to certain staff scientists and those in technical roles. Therefore, institutions are responsible...suggested that the salary level should now be automatically adjusted every 3 years. In May 2016, Secretary...requirements of the FLSA. In the University of California system, the postdoc union has negotiated a raise...likely the number of postdoc positions in the biomedical enterprise in the U.S. will decrease. At Future...has clearly not been a sustainable approach to biomedical research in the U.S. and postdoctoral training...academic system is increasing, and becoming ever more critical. In 2016 not only were postdocs not exempted from...

...position at Addgene, the skeptical applicant asked if she would partake in “critical thinking” in the position... away from calling non-academic careers and desk jobs “alternative careers.” Realistically, based on the...it. The opportunity to be creative and think critically. One of the very first times I interviewed a ...wish for a stretch of time that doesn’t involve critical thinking. Former Addgenie Jessica Welch says, ...aspect of their chosen career. You can confidently call yourself a Scientist. You work in a lab. You formulate...transferable skills. Transferable skills are the non-technical skills you pick up wherever you work, and you’... communicating. After years of focusing on my technical skills with cloning and lentivirus production,...

... prep library. Addgene’s pooled libraries are typically DNA preps, but we do distribute several of our...larger lentiviral preps can be used for screening-scale transduction of cells, resulting in cell population...The size and composition of your library can drastically impact what conditions it needs to properly amplify...can transduce your cells.  While Addgene uses a physical titer (via ddPCR) to quality control our viral...include a 1.3 mL aliquot with mostlibrary requests specifically to allow scientists to perform functional titering....  Resources and references References Genome-scale CRISPR-Cas9 knockout and transcriptional activation... useful place to ask experimental questions.  Practical Considerations for Using Pooled Lentiviral CRISPR...

...preference.   Historically, ICSS was done by implanting an electrode and non-specifically electrically stimulating...the steps and technical considerations are directly applicable to the rat [6]. Technical differences include...[2]. Laser activation is usually controlled automatically using motion capture software such as EthoVision..., regardless of the type of behavior, certain technical considerations still apply. Testing stimulation...is wrong or 2) there is some problem with the technical implementation of your optogenetics setup (viral.... 8.Han, Xue, et al. "A high-light sensitivity optical neural silencer: development and application to...

...signals from these reporters. Lack anatomical context/spatial localization: In vivo imaging with fluorescent... be overlaid onto anatomical ultrasound imaging to show where the bacteria localize in relation to internal...ultrasound fingerprint can be detected. Bourdeau et al calls this method acoustic collapse.  Importantly, acoustic...exciting application for ARG’s: in vivo imaging. Specifically, arg1 expressing E. coli aided in ultrasound...intestinal tract and has been used for 100 years to clinically treat enteric infection and inflammatory bowel..., but lux imaging shows only that the bacteria localize to somewhere in the mouse abdomen. arg1 signal...

...promoters and Shine-Delgarno sequences used in this so-called bicistronic design (BCD). The 49 vectors in this...: Čelešnik, Helena, et al. "Biosafety of biotechnologically important microalgae: intrinsic suicide switch... Rogers, Jameson K., and George M. Church. "Genetically encoded sensors enable real-time observation ... Ribosome-Controlled Fluorescent Reporter."ACS chemical biology 11.1 (2015): 31-37. pCri system The Gomis-Ruth...latency in matrix metalloproteinases." Journal of Biological Chemistry 290.8 (2015): 4728-4740. You can find...The gene set was carefully chosen to perform statistically relevant benchmarking of cell-free expression...Marx's lab has engineered and validated a new method called FREQ-Seq. This strategy allows scientists to construct...

...2012) scFv Antibody: Principles and Clinical Application. Clinical and Developmental Immunology 2012:1...being smaller than antibodies. scFvs are often genetically fused to other proteins, which has led to their...with 10-24 copies of the short epitope GCN4, also called a scaffold; and 2) a GCN4 binding scFv that’s fused...is easier and cheaper to generate since it’s genetically encoded.   Translational applications of scFvs...antibodies, there are many scFv-based therapies in clinical trials or already in the clinic (Bates and Power... tumour specific antigen. When these molecules, called Bispecific T-cell engagers (BiTE®s), bind CD3 on...David vs. Goliath: The Structure, Function, and Clinical Prospects of Antibody Fragments. Antibodies 8:...

...covered in detail here. Classical double-strand break repair (DSBR) In the classical DSBR pathway, the 3’...and Homology Directed Repair (HDR). NHEJ is the canonical homology-independent pathway as it involves the... provided the DNA template used for repair is identical to the original DNA sequence at the DSB, or it...plasmid, etc.), and consists of three pathways: classical double-strand break repair (DSBR), synthesis-dependent...purple arrows) or on the non-crossing strand (vertically at the orange arrows). If resolved dissimilarly...applicable in DSB-induced genome engineering, it has biological importance for the repair of breaks that lack...2281-308; (2013). PubMed. A Mouse Geneticist's practical guide to CRISPR applications. Singh P, et al. ...

...University of California, Irvine University of Massachusetts, Worcester  University of Nebraska Medical Center...University and Medical Center  Weizmann Institute of Science Whitehead Institute for Biomedical Research ...time of request MTAs and deposit agreements to basically instantaneous in many cases.  Suggest that they...your organization below? Don’t worry--we check periodically for possible new awardees, and we’re happy to...Hospital  Brandeis University  Broad Institute  California Institute of Technology Cold Spring Harbor Laboratory...University Rockefeller University  Salk Institute for Biological Studies The Scripps Research Institute St. Jude...

..., soon directed himself to finding “immunological and virological solutions to crises like those and ended...Therapeutics, which was acquired by Ultragenyx Pharmaceutical in 2017. As one of the original employees at...learned more about Addgene. “The mission to share critical reagents such as plasmids and viral stocks for...depositor. KSQ uses a CRISPR-Cas9 platform to systematically test the function of all 20,000 genes in disease...Target Discovery at the Novartis Institutes for Biomedical Research. Drug development was something Stegmeier...genetics.” As a postdoc in Stephen Elledge at Harvard Medical School, he developed the first lentiviral microRNA-based...Associate Professor at Mass Eye and Ear and Harvard Medical School (HMS) where he leads a lab of 25 people....

...Python script called SSFinder, but I find its implementation to be too slow for practical use. The R based...causes malaria). I attribute their success to technical expertise, thoughtful single guide RNA (sgRNA)...the piñata builders - the reviewers. After some physical exertion on the part of the party goers, the piñata...the other hand some software tools make use of empirically derived and/or prior knowledge to inform on the... Hsu et al., 2013) used a combination of both empirical and approximate methods. The details of their ...“high mismatch limit”, “approximate design”, “empirical design”, “single-PAM design”, and “multi-PAM design...sites, scores and the statistics that go into calculating them. For this, some online tools such as Cas-OFFinder...

...Talley Lambert, a Research Associate at Harvard Medical School. The need for a community fluorescent protein...one of the most indispensable tools in modern biological research.  Any microscopist will tell you that...maturation, oligomerization), many of which are dramatically affected by environmental conditions (such as... structure was needed.  It is also difficult to scale such a resource when updates depend on a single ...feature filter spectra and collection efficiency calculations.  With ~80 FP spectra (and rapidly growing, ...Talley Lambert is a Research Associate at Harvard Medical School. He manages the Cell Biology Microscopy ...Microscopy Facility, specializing in advanced optical microscopy. Follow him on twitter or github @tlambert03. ...

...form of many, many short DNA sequences called reads. Typically they’ll be in a file in FASTQ format, a...DNA is needed for screening experiments, so the scale of the DNA prep is larger. And since the library...all components of the library are represented. Typically, Addgene uses electrocompetent Stbl4 cells when...ensure a good transformation efficiency. For a typical library, Addgene usually does four to eight electroporation...product because the plasmids in the library are identical except for the insert; there’s no need to sequence...). You can also rank the plasmids by abundance, scaled to 1, to create a “cumulative wealth distribution...distribution” curve, or Lorenz curve. By calculating the area under the curve (AUC), one can gain a sense of the...

...quick turn-around time of Sanger sequencing have historically matched the needs of most molecular biology ...rapid advances in technologies that permit large-scale creation and synthesis (“writing”) of longer pieces... a collection of 96 plasmids on a plate) will typically have a wide range of input quantities. This variation...samples. As mentioned above, one of the primary technical benefits of plexWell™ is that normalized libraries... proprietary chemistry). This turns out to be critically important for getting adequate sequencing depth...via plexWell™ libraries is well suited to large-scale de novo assemblies of short constructs like plasmids...computational biologist with a passion for solving critical sequencing problems. He received his PhD in Bioinformatics...

...Arabidopsis (CIBN), which they call the LADL Anchor. Using specifically designed gRNAs, they can then ...Inducible Degradation (AID) uses plant hormones called auxins to conditionally and reversibly degrade ... for AID. By tagging proteins with a 7kD degron called mAID and expressing the essential plant protein...microorganisms based on metagenomic data. MerMAIDs (Metagenomically discovered Marine, Anion-conducting and Intensely...publicly available metagenomic datasets with biophysical studies and the potential of mining datasets ...transcription factors tethered to dCas9, require long time scales with constitutively expressed proteins that are...nature of genomic looping due to it’s briefer time scale and its inducible and reversible nature. Find the...

...scene. But what about the other yeasts – in the biomedical world, are there even other yeasts? In this blog...The most commonly used yeast by biotech and pharmaceutical companies is K. phaffii (formerly known as ...the system. Since then, multiple biotech and pharmaceutical companies (along with some research laboratories... bread. The following table lists some of the biological commonalities and differences between K. phaffii...the expression of recombinant proteins by the pharmaceutical and biotech industries as a protein expression...modification of recombinant protein products, specifically glycosylation. The native glycosylation machinery...human: The important gene co‑expression modules. Biomedical Reports 7.2 (2017): 153-158. DOI: 10.3892/br.2017.941...

...lentivirus and have been difficult to manipulate genetically. To solve this issue, Sarah Teichmann and colleagues...triglyceride or cholesterol contents (what is commonly called bad cholesterol). However, size distribution and...including quantification of abundance, size, and localization in vivo. The LipoGlo system represents a new... (bEBPs) at a sequence upstream of the promoter called the upstream activating sequence (UAS). The Wang...Communications, 2019. PubMed PMID: 31451697. Genetically encoded voltage indicators for use in worms Article... Article contributed by Brook Pyhtila Genetically encoded voltage indicators (GEVIs) change fluorescence...real time when neurons or muscle cells transmit electrical information. Such voltage imaging can be performed...

...different signals in a certain region or calculate a colocalization factor to assess the spatial relationship...microscope to see where the target protein is (localization) and how much there is (quantification). But...protein targets and you want to know if they co-localize at the same place in the cell? Or you know that...inactivate the fluorophores in the sample, either by chemical treatment or photobleaching or by stripping out...yourself stuck with red-green images generated automatically from the microscope software, you can always...it, the secondary antibody may be binding non-specifically – try optimizing your blocking and washing conditions... your multiplex-labeled sample to see if the localization and intensity patterns are similar between the...