...more and more students are asking. Teachers are also asking, “How do I engage my students in real-world...the study of synthetic biology into the hands of students and teachers in the U.S. and beyond. “I want to...programs all focused on current questions and experiments in the field of synthetic biology. Founded as...excitement found through experiential learning. “Students may forget the technical details they hear in ...their classes,” she said, “but they remember the moments when they discover something new for themselves...asked in MIT’s research labs, BioBuilder inspires students and teachers to apply engineering principles to... biology and transforms them into modules that students and teachers can investigate together. Teachers...

... This means they do not reliably detect editing events that occur in less that 5% of the population (Fu...standardized thresholds for validating CRISPR experiments, many are turning to next-generation sequencing...genome predicted to contain off-target cleavage events. Unbiased techniques search the whole genome for...Frequencies of off-target mutations are essential data points for investigators looking to definitively link ...irreproducible data in a research setting, but these events could have disastrous health effects in the clinic...current algorithms do not take into account other elements, including those relating to DNA structure (e....and HTGTS (Frock et al. 2015) for cell-based experiments. These strategies can be used in concert with...

...threshold requirements: (1) that you have international recognition for your outstanding achievements in your...whenever you have new accomplishments to add. Obtain copies and translations of documents that are not in English... candidate meets the requirements set forth by USCIS before engaging with clients. To learn more, visit..., Esq. Founder of Casseus Law. Disclaimer: The contents of this post are intended to convey general information...and not to provide legal advice or opinions. The contents of this post should not be relied upon for legal...presented may not reflect the most current legal developments.  Further, this post may contain technical inaccuracies...actions taken or not taken based on any or all the contents of this post.  An attorney should be contacted...

...CRISPR experiments that involve HDR, electroporation can be combined with cell-type specific reagents in ...RNP-mediated CRISPR experiments While using Cas9-gRNA RNPs for CRISPR experiments can reduce many potential...result, RNP mediated CRISPR experiments may not be suitable for experiments where stable Cas9 expression...experiment requires delivery of, at minimum, two components: the Cas9 protein and a guide RNA (gRNA) targeting...are many advantages to using RNPs for CRISPR experiments. The RNP method can often be used in cells that...generation or homologous recombination.  However, experiments that require long-term expression of Cas9, such... by commercial vendors such as IDT. These two components are then incubated together to form the RNP. ...

...Kim et al., 2017 SaBE3, BE3 PAM variants, BE3 editing window variants   Greatly expands the number of ...editing work? Base transition editing requires three elements. They are, broadly: A Cas protein (catalytically...editing window specified by the Cas protein These elements were the starting point towards the development...inhibitor of uracil DNA glycosylase (UGI) to dCas9 prevents base excision repair, which would change the U...development of BE3, many research groups have made improvements to base editors, including: expanding targeting...upstream of the PAM.  David Liu’s lab generated BE3 variants with other deaminases: AID, CDA1, and APOBEC3G... Liu lab also used natural and engineered Cas9 variants to develop five new base editors with distinct...

...with two measurements: forward scatter (FSC) and side scatter (SSC). To acquire these measurements, the cytometer...precisely measure your cells of interest. In many experiments you’ll be working with a heterogeneous cell population...describe the shape of a histogram, which graphically represents the time and intensity of the cell’s illumination...cytometry can be used for virtually all kinds of experiments and research fields, for any experiment, your...cells, the single cell gate to exclude duplicate events, and the Live/Dead gate to focus your analysis ... As an example, we’ll use one of my previous experiments where I harvested a melanoma tumor from a C57BL...my lymphocyte population (10.7% of all recorded events) based on their expected size. The strong signals...

...work with your colleagues, supervisors, clients or even students, your ELN should allow you to collaborate...paper-based record keeping barely copes with the growing amounts of digital data generated in labs. While many labs...different ELN features, ranging from whether respondents saw them as not important to very important. ...explored the barriers to adoption within academic environments to better understand the issues labs are facing...limited budgets, “a large percentage of survey respondents indicated that cost was a significant barrier...system within their institution. In the study, respondents were also asked about how important ease of use...from paper to digital for example): “… 99% of respondents indicated that ease of use would influence their...

... your protocols, designed your experiments, and prepared your reagents. You’re going to engineer the best...assemble up to 6 different fragments in a prescribed order. These fragments can be pooled in one tube ...PCR to generate DNA fragments with 15-40 bp of homology at their ends. These fragments are then combined...methods are more amenable to combining multiple DNA fragments than others. In today’s post, we will focus on...in an hour or less. The ligations combine the fragments in an order determined by their homology. You ...cloning process. Time spent actually doing the experiments are also generally comparable so the best way...optimize reagent concentration, or purify DNA fragments from gels. If you’re relatively new to the cloning...

...problem.  Pre-block with Fab fragments (Figure 2C) Speaking of Fab fragments… Another strategy for species-on-species...been bound up by the Fab fragments. Note that you should plan to use Fab fragments that are from the same...should not recognize Fab fragments from the same species and 2) these fragments will be more likely to ...include no primary antibody controls in your experiments. If you do find high levels of background staining...that is directly conjugated to your reporter circumvents the issue. However, directly conjugated primary...pre-treating the tissue with unconjugated Fab fragments that recognize the endogenous IgGs (Lu and Partridge...Partridge, 1998). After washing away unbound fragments, you can then apply your primary and secondary antibodies...

...Complex experiments Finally, additional controls may be required for more complex experiments. A multiplexed...helpful to focus on something controllable, like experiments (and their controls!). This blog post will discuss... the ins and outs of controls for biological experiments, starting with general controls and then moving...design thoughtfully and thoroughly controlled experiments.  Broadly useful controls Positive and negative...negative controls Most biological experiments require positive and negative controls to ensure proper interpretation...group.     Figure 1: A, Most biological experiments will benefit from positive (+) and negative (...group and C, technical replicates or repeated measurements will increase the power of the results. In this...

... antibodies in plants using syringe agroinfiltration." Recombinant proteins from plants. Humana Press,...candidate at Northeastern University. Working with plants doesn’t always have to be a time-consuming process...reproducible. Prior to creating transgenic cultures or plants, our transient expression method enables us to ...leaf transformations The development of transgenic plants is a common problem in non-model organisms. Therefore...choice for investigating gene function, as these experiments can be done in days to weeks instead of months...roseus. A common method for overexpressing genes In plants like Arabidopsis and tobacco, Agrobacterium infiltration...more easily quantify the effect of the different treatments on transformation success. Some reporter gene...

...curate reagents from these emerging organisms so scientists can easily find the useful new reagents that...Cnidarian-Dinoflagellate symbionts (Virginia Weis) Sea anemone Aiptasia - algae Breviolum minutum symbionts are important...Westwood) Dodders are parasitic plants that steal all their food from other plants and are unusual enough to...between gene function and phenotypes in diverse plants, animals, microbes, viruses, and fungi for which...for scientists and educational programs for K-12 students. You can see why I was excited to be invited to...at least 6-7 times and on at least 2 separate continents. Mimulus (Andrea Sweigart) Monkeyflowers were...and Asclepias curassavica (Gerog Jander) Milkweed plants are known to many as the only Monarch butterfly...

...many microscopy experiments with fluorescent proteins (FPs) localized to compartments other than the cytoplasm...misfolded FP-fusions on quantitative imaging experiments and cell physiology in general. Pitfalls of Fluorescent...apparent and can confound quantitative imaging experiments or even negatively impact cells (see Figure 1...sequences, which often have absolute position requirements. For example, a KDEL ER retrieval sequence only...that FPs are often poorly suited for cellular compartments other than the cytoplasm. Generally, FPs evolved...in or were engineered for use in cytoplasmic environments. However, approximately 40% of human (and most... localize to chemically distinct subcellular environments, including the organelles that compose the secretory...

...conditions. Purifying DNA fragments Once you’ve generated your DNA fragments, it is always a good habit...digested fragments or PCR products from a gel. You will avoid contamination from other DNA fragments and you...nanodrop to assemble the  fragments based on their molar ratio. Assembly of the fragments There are multiple ... way to do it (i.e. avoid assembling too many fragments at once, if it is possible). There are many softwares...could affect or delay your experimental work. Fragments generation After you’ve designed your cloning ...cloning scheme, you’re now ready to generate fragments. You can generate the parts of DNA that you want to assemble...between the different enzymes. Always check the fragments size of your digestion on an agarose gel. If the...

...neuron subtype) and specific subcellular compartments for measurements. All of the sensors discussed below ... you are measuring the events-of-interest. Sensors suitable for ER measurements include: CEPIA (additional...are used to monitor calcium concentrations and transients in living cells and organisms. Unlike chemical...slower). GCaMPf may be suitable for very rapid measurements, like action potentials in neurons. jGCaMP7 ...calcium concentrations in different subcellular compartments can vary greatly. Additionally, the calcium ... the (1) binding of calcium, (2) allosteric rearrangements of the sensor, and (3) subsequent change in...you combining your calcium reading with other measurements, specifically fluorescent ones? Many of the ...

...uniquely challenging to apply in dicotyledonous plants, or dicots. But Jae-Yean Kim’s lab recently "broke... strategy uses new combinations of PE protein components (Figure 1), an altered epegRNA delivered with...chaperone, RT: reverse transcriptase. Right: T1 tomato plants that inherited an edited gene to confer resistance..., two weeks after herbicide was applied to both plants. Adapted from Vu et al., 2024 bioRxiv, under CC-BY-NC-ND...both tomatoes and Arabidopsis, suggesting the improvements may be broadly applicable to dicot species. .... In addition, they generated offspring tomato plants that inherited the genomic edit but not the editing...desired edits in tomato and Arabidopsis. Nature Plants, 10(10), 1502–1513. doi: https://doi.org/10.1038...

...electrophoresis. Smaller fragments migrate quicker than larger fragments. These fragments are quantified over...the DNA such that smaller fragments are quantified first before larger fragments. Figure 1: The quantification...units over time. Smaller fragments migrate more quickly than larger fragments. Image from OpenWetWare....your DNA prep and whether there are any other contaminants. Nucleic acids (DNA and RNA) absorb maximally...quick and simple and doesn’t require any special reagents. However, there’s limited sensitivity at low concentrations...piece of DNA. This method is best used for DNA fragments (like a PCR product). This method also gives an...a few minutes per sample. During the run, DNA fragments move through a micro- or nanofluidic channel and...

...literature. Data reported from flow cytometry experiments can be a little challenging to understand if ... and output is generated through measurement of events. An event is something that passes through the ...axis to generate a dot plot (Figure 1). Clustered events are called a population.                           ...left, it might make more sense once you realize events are plotted on an invisible Cartesian plane (right...real-world data is far messier than biorender plots, quadrants can still help me as a reader if I'm struggling...strategy from Barlow-Anacker et al., 2017, with quadrants to help visualize the different populations. Used...populations; this indicates the percentage of total events contained in the gated population. Heat maps are...

... protocol or reagents, do you understand all of the steps? Do you know how the reagents have been validated...preparation) A history of successful funding (fellowship grants) A project with sufficient preliminary data to...couple of months and requires that all of the experiments have been completed. Therefore, to be ready to...postdoctoral mentor. A good mentor typically writes the grants that fund your research, guides the research directions...provide expertise in designing and interpreting experiments, as well as career guidance. In my own experience...the methodology and can have confidence in the reagents and outcomes. This is preferable to finding out...work for your specific assay. "Quick and dirty" experiments often eat far more of your time as they can result...

...fluorescence imaging strategies use widely varying amounts of excitation power (Shaner et al, 2008). In confocal...to predict how fluorophores perform in ‘real experiments’, it is advisable to perform time-lapse imaging...with low excitation power. By repeating these measurements for different fluorescent proteins and by comparing...protein distribution. Therefore, photostability measurements can be performed with soluble fluorescent proteins.... It should be noted that the photostability measurements reported in the literature are performed in ... the experimental designs used to make these measurements and hope this information can help guide your...evolves over time. The second issue is that, in experiments that measure photostability, high excitation ...