...editors (CBEs) and adenine base editors (ABEs) chemically modify target bases without breaking the DNA ...one-ring pyrimidine base. This is a far more complex chemical task, not a job for a single enzyme. Base ...editing works in general. Base editors use either catalytically dead Cas9 (dCas9) or a Cas9 nickase (nCas9) ...adjacent DNA to create a region of separate strands called an R-loop (Figure 2). This allows the guide RNA...terminology when discussing base editors, like calling it the “edited strand.” Uracil excision repair... an engineered adenosine deaminase capable of chemically converting adenosine (A) to inosine (I, treated...converting the C base to uracil (U). This is the same chemical reaction performed by CBEs. However, most CBEs...

...fixatives - chemical cross-linkers and organic solvents.  Chemical Cross-Linkers Chemical cross-linkers...artifacts and how to minimize them. FocalPlane. https://focalplane.biologists.com/2020/07/07/fixation-artifacts-and-how-to-minimize-them...-linking cellular proteins. Cross-linking is a chemical reaction that covalently joins two molecules and... confusion. Paraformaldehyde: Many IF protocols call for paraformaldehyde (PFA) as the fixative. PFA ...depolymerizes, producing formaldehyde. Often people will call the resulting solution PFA, but it’s really just...proteins can be lost during fixation with these chemicals, which impacts sample structure and could also... target to be washed away. Furthermore, these chemicals can also alter the structure of proteins, which...

...BglBricks: A flexible standard for biological part assembly. Journal of biological engineering. 2010;4(1):1. Pubmed... diverse functions, and thus, is used in many biological fields. In synthetic biology for example, high-throughput...elements to generate non-natural tools such as novel biological circuits or sensors. Given the expanding palette... can be used to detect structure and protein localization, as well as cellular processes like gene expression...in-frame to a tethering partner, which directed localization of the fluorophore, and thus enabled labeling...emission maxima Tethering partner Subcellular localization 1 TagBFP 399nm/ 456nm histone 2B (H2B) Chromatin...to generate polycistronic containing multiple identical polyadenylation signals or promoters Gibson et...

...al.: bowtie2 -f -x HG19_GENOME --local -f -k 10 --very-sensitive-local -L 9 -N 1 -U GRNA_23MERS -S GRNA_HITS.sam...genomic regions that are bound to modified proteins called histones. We can detect modified histones with ... Table 1. Because of DNA’s 3D geometry and the chemical properties of modified histones, a genomic region...maintaining ESCs. So which of these 13,000 regions are critical? One hypothesis: the enhancers! This leads us ...approach for designing an experiment to identify the critical NANOG binding sites: 1. Find Enhancers that have...differentiate Step 3 reveals which NANOG-related genes are critical to stem cell survival. Knowing which genes influence...and therapeutics. We’ll have more to say about clinical applications of CRISPR in the next section. In...

... We’ve also created constructs with containing chemical tags such as the SNAP-tag, Halo-tag, and CLIP-...animals and fix the samples. When you use AAVs, it typically takes a few weeks to achieve optimal expression... Any longer and the cells may start to show morphological abnormalities due to the excessive amount of... levels of XFPs - Reduce the amount of tTA. Paradoxically, too much tTA leads to a reduced expression ...most likely by suppressing transcription. It is critical to express a minimal amount of tTA to achieve ...brain samples, we recommend pretreatment with ScaleCUBIC1 (Susaki et al., 2014), before clearing with SeeDB2...sensory systems focusing on the functional and anatomical maturation of the olfactory system.      Takeshi...

...get there and more practically, when do you need to be there? A typical biomedical postdoc fellowship ... fail to replicate. Plan experiments logically and strategically to increase your rate of productive results...theJanelia Research Campus of the Howard Hughes Medical Institute. Today's postdoctoral fellows (PFs) face...submitted manuscript in a high-profile journal typically takes 6-12 months depending on the revisions and... to be ready to write by Year 3.5. Thus, it is critical to get an experimental system up and running very...identified a postdoctoral mentor. A good mentor typically writes the grants that fund your research, guides...However, you have finite time and resources. You typically have 4-5 years to make discoveries and publish...

...circle. Typically, a yellow check mark indicates that a particular parameter was automatically adjusted... The vertical black dotted line represents the cut site. Cutting and error-prone repair typically result... of robust software tools. As a consequence, a critical step in the gene editing workflow - analyzing ...over-looked.  Synthego has developed a new tool called ICE (Inference of CRISPR Edits) to solve this problem...guide RNA sequence you used. The ICE tool will calculate overall editing efficiency and determine the profiles...and interpret data about these types of edits is critical to the CRISPR workflow. For a multiplex sample...steps to learn. For increased flexibility and scalability, the ICE software has two analysis formats: sample...

...dissonance (Kunda, 1990). More specifically, they were engaging in a behaviour called the “biased evaluation ... past my bedtime, poring over my grandparents’ medical textbooks by torchlight under the covers. In high...boasted to me that he never eats “anything with chemicals in it,” leaving me to wonder how he has survived... read a version of the abstract where the real medical conditions had been swapped with made up illnesses...their preconceived ideas about the controversial medical issues. Participants gave significantly more favourable...beliefs even though all three texts were otherwise identical. Likewise, when participants read an abstract ...rate that study as untrustworthy, inaccurate, methodologically flawed, and biased. As a result, the control...

... or poor scalability.  Scientists at Janelia Research Campus and the University of California, Berkeley...across broader physical areas of the brain and enable access to neurons that are physically blocked, such...driven by neurons. By studying how neurons are physically connected, we can begin to understand how the...Therefore, by simply looking at how neurons are physically connected we can begin to understand how the ...region (anterograde tracer, Fig. 1B). Tracers are typically delivered to a particular location and they either...retrograde tracer) (Fig. 2). Viruses as neuronal scalpels Viruses can be injected into the brain and efficiently...neuronal signaling, or manipulating any other genetically controlled function. By using AAVrg in Cre transgenic...

...protein. The electrical system converts the fluorescence intensity to a voltage pulse, called an event, ...of the population as a whole, scientists gain statistical power in their observations. However, while flow...subcellular analysis such as morphology or subcellular localization studies. For these, alternative methods such...Cells are first resuspended in a pressurized buffer called sheath fluid and transported through tubes or capillaries...in single-file where it is interrogated by the optical system (Figure 1).   Figure 1: Cells expressing...complexity, measured using visible light scatter The optical system has both visible and fluorescent light sources...same direction as it was initially traveling is called forward scatter (FSC) and provides information ...

...compute using electrical impulses to coordinate emotions, thoughts, and behavior. Historically, scientists...To bring greater control to Acr activity as a biological tool, Niopek and colleagues turned to optogenetics...fusions, and xCas9, and requires no additional chemicals or modifications. This versatility opens up the...scientists study the electrical activity in the brain by inserting electrodes into the brain. But this process...and expensive. Thus scientists have turned to genetically encoded voltage indicators. To expand the voltage...thousands of proteins for one that can report electrical activity via imaging. They took the light-sensitive...light-sensitive protein QuasAr2 and systematically mutated it. Using a robotic picking approach to select cells...

...working on new experimental and theoretical methods to push the scale of genetic engineering, with the... genomic scale, with the expectation for major advances in agriculture, materials, chemicals, and medicine...to get everything to the scale of building synthetic genomes or genome-scale construction projects. Not... make a very large number of regulators. That basically means larger genetic circuits that could conceivably...material as sophisticated as wood. To build at that scale, we also have to think through programming cells... ground up, but so that genetic designs of that scale could be created. Someone could take on an engineering...resource control - everything that’s necessary on that scale.  If you look at what we’ve already put in, the ...

...in their ability to be specifically and potently activated by pharmacologically selective effector molecules...wiring of the brain and the underpinnings of neurological disease, neuroscientists need to be able to ...What is chemogenetics? Chemogenetics relies on genetically introducing engineered receptors that are only...co-developed by Bryan Roth's and Takafumi Minamimoto's lab called deschloroclozapine (DCZ) shows promise as a CNO...et al., 2019). Using PSAMs PSAMs PSAMs, or pharmacologically selective actuator modules, were developed... such as varenicline, are already approved for clinical use. Varenicline has been further modified to ... create ultrapotent PSEMS (uPSEMs) that have drastically increased potency. Download our chemogenetics...

...formulating new biological concepts. However, rates of reproducibility for preclinical studies, as reported...on solutions to reproducibility issues in the biological sciences and featured speakers from academia,...Overview - Jeffrey S. Flier, Researcher at Harvard Medical School, former dean of the faculty of Medicine ...2017 and Schmmidt 2009, but for our purposes we’ll call a study reproducible if its findings can be predictably...to your own research and thereby help move the biological research enterprise towards greater reproducibility...experiment, you’ll need to analyze your results. As biological researchers deal with larger and larger datasets...stories has, however, made it difficult to publish so-called “negative” results that conflict with our original...

...responsivity in screening ASAP3 variants. B) Electrical and optical recordings of spontaneous activity in human...protein-coupled receptors (GPCRs) are critical components of many physiological pathways and represent the largest...GPCR. Example applications include large-scale pharmacological profiling or interrogation of context-dependent... created ASAP5, a faster and more responsive genetically-encoded voltage indicator (GEVI) than previous...mEPSPs has been possible with conventional electrophysiological methods, it has remained difficult with ...largest family of human drug targets. To enable large-scale profiling of many GPCRs, Mikel Garcia-Marcos’ lab... collection of BRET-based ONE vector G-protein Optical (ONE-GO) biosensors (Janicot and Maziarz et al....

...research? I grew up knowing little to no biological or biomedical scientists and had no idea what the daily... global problems. Biomedical research, for instance, contributes heavily to medical practice, and understanding...the Daily Psychological Experiences of First-Generation College Students. Social Psychological and Personality...hazardous liquids. Working in a lab is nothing like a typical part-time or 9-to-5 job. I had to ask to find out...In basic science (as opposed to translational, biomedical, or applied sciences), people conduct research...with what happens in the lab Official title is typically Professor, Assistant Professor, Associate Professor...project. Lab technician / Research assistant Typically has a Master's or Bachelor's degree Generally ...

...pAAV-hSyn-mCherry Read on to learn more!  Calcium sensor AAV The GFP-based calcium sensors are single-wavelength ...Addgene! Archon1, a voltage sensor AAV Historically, electrical activity in the brain was measured with...sensors with intensities that change in response to calcium binding. There are a few versions of these jGCaMP7...brightest resting fluorescence of the GCaMP7 family of calcium sensors and can be used for imaging of small neuronal...variant of jGCaMP7 in AAV1 at Addgene! See all calcium sensor AAV at Addgene. GABA sensor AAV GABA is ... directly imaging GABA have been limited. Like calcium sensors, different iGABASnFR have been developed...(pAAV.hSyn-FLEX.iGABASnFR) has good membrane localization and brightness. The F102G variant (pAAV.hSyn-FLEX.iGABASnFR.F102G...

...nuclear localization of fluorescent proteins, they found that adding a triple nuclear localization signal...fluorescence protein-based calcium sensors (jYCaMP1), variants of the calcium indicator jGCaMP7, that are...with red fluorescence protein-based calcium sensors. These new calcium sensors include syn-jYCaMP1s (slow...purified recombinant proteins at small and large scale.  This new technique involves selection in the cytosol...compartments in mammalian cells By Angela Abitua Genetically encoded fluorescent proteins are often used to...specific structures, compartments, or specific localization of biomolecules within cells. However, sometimes...sometimes these fluorescent proteins might not localize to the right places, which can provide misleading...

...to develop strategies to make our classes more practical and hands-on. Students in these courses get plenty...quick flashback to time spent playing a card game called “Magic”. There were complicated rules that governed...upon who your challenger was, you might have to drastically alter your strategy. I realized that similar ...engineering and strategic knowledge to solve a clinical disease case. As a teacher, you explain the game...strategies while noting any gaps in their knowledge. Practically speaking the format I decided on was to have ...of 4 people face each other on a single chosen clinical disease case. Then, each team received a whole...build a transfer plasmid that could be used to genetically manipulate human stem cells. Then they had 10...

...Research Fellow with Pamela Silver.  Most types of biological motion (whether endocytosis, vesicle trafficking...it to suit our purposes? In search of simple biological machines R bodies can repeatedly extend and...R-bodies, check out this video. Most types of biological motion (whether endocytosis, vesicle trafficking...to pH changes without the need for ATP or other chemical fuel sources. Like an actin filament or a microtubule...polymers, however, R bodies do not exert force by dynamically rearranging into different polymerization states...body monomers respond to pH changes by undergoing local conformational changes. These tiny movements are...by propagating through an enormous lattice of identical subunits. A brief history of R bodies R bodies...