...deconstruct and understand this complexity using existing C. elegans mutants. For instance, we use a mutant...research on worm locomotion, but our worms are constantly moving so we need good ways to monitor and track... C. elegans molecular biology are based on the standard worm genome. While C. elegans are often thought...and so far most of their funding has come from kickstarter and fundrazr projects). This allows the project... to a wider group of people. This is a perfect starter project for our computer scientists, many of whom...interested in biology but don’t really know how to start applying their skills to it. The Kittybiome project...Funding Makerspaces One of the main challenges when starting a new project at a makerspace is finding the financial...

...number is then determined by comparing results to a standard curve. For CNV assays, it is recommended to use... (Ma, 2014.) As with all qPCR assays, samples, standard curves, and normal controls must be run in triplicate... the variance seen within multiple runs of the standard curve. Signaling molecules: Sybr Green and Taqman...noise, due to the large amount of dsDNA in most starting materials, and is not particularly sensitive. ...each reaction, math happens (this time, Poisson statistics), and the readout gives an absolute value of ...concentration values, rather than by comparison to a standard curve, and most results can be confidently interpreted...Bell, 2018.) Even though it does not require a standard curve or a normal control, it can take a few hours...

...plants, and agricultural crops in particular, resistant to disease. They also devise biosensors designed...that they work well in plants and give similar stability to transcripts as the ones that people use all...all the basic and necessary elements in order to start using the MoClo system. The paper also gives quantitative...have any particular tips for those looking to get started with MoClo? Patron: The parts will be familiar ...the parts that you need from the kit and getting started making your own constructs with Golden Gate MoClo...conceptual barrier. Sometimes people don’t know how to start. They might want to use our promoters and terminators...they don’t have any prejudice about it. They just start and go ahead. I can see science speeding up. Addgene...

...verify the starting methionine of a gene but the blastx results start the alignment at a more distal amino ... available, we primarily use Standard Nucleotide BLAST (blastn), Standard Protein BLAST (blastp), and ...Translated BLAST (blastx). NCBI has a terrific getting-started guide for BLAST, which includes a simple explanation...differences below. Optimizing blastn searches On the Standard Nucleotide BLAST page, the first decision to make...homologous regions, which by default are ignored in a standard blastx search. An alignment omitting repeated ...the sequencing result, we often choose between a Standard Protein BLAST (blastp) and blastx search to verify...sequence alignments that BLAST is unable to handle, Clustal is our frequent choice for pairwise or multiple...

...knockouts.   Star Trek: Into Darkness (2013) which is the remake of the space-melodrama Star Trek II: The...into the twenty amino acids. Once scientists established that DNA encoded all the information necessary...were exploring were space and robots. Warping to stars in space ships and the rise of killer machines that...Released in 1997, GATTACA is an American SciFi film starring Ethan Hawke, Uma Thurman and Jude Law. The movie...novel, Inferno (2013) and the movie version (2016) stars Tom Hanks as the protagonist (Langdon). The plot...engineering in the recent SciFi movies. Rampage (2018), starring Dwayne “The Rock” Johnson, calls out CRISPR as...pegRNA (prime editing RNA), the prime editor can install all possible point mutations, delete short stretches...

..., such as the starting material (DNA-based vector or purified RNA) and the initial state of the dsRNA ...experiment functions as the building block of our understanding of complex biological processes. Many tools ... knockouts have long been considered the “gold-standard” for LOF studies, the high gene copy number found...function due to the use of exon skipping, alternative start codons, and/or the phenomenon of transcriptional...transcriptional adaptation (Smits et al., 2019; Sztal and Stainier, 2020). Additionally, a study that directly compared...approaches and considerations present at the first stage of an RNAi-based investigation. Creation of the ...gene silencing efficacy, thereby requiring a substantial time investment. Once the target mRNA is cleaved...

...special about her pure interest and curiosity to understand my work and me, especially as much of her focus...environment filled with people who are interested in understanding the work you do, in addition to being genuinely...bigger projects I was tasked with was creating and sustaining a biweekly report of our social media analytics...Addgene before. This meant I was responsible for establishing a new report and routine across the marketing...excited but overwhelmed; I had no idea where to start. Thankfully, my managers set aside time for me to...template to build out a report on. I was able to understand what metrics would be useful and how to organize...with the larger content and marketing team, and I started preparing for my first official professional presentation...

...work gets done Managers do this by removing obstacles that stand in the way of the doers and by ensuring ...just have to know it when you see it? “The Three Stages of Your Career: Doer, Manager, Leader” by Charlotte...importance of these very different roles. At any stage in our careers we may be in a cycle of doing, managing...are the ones who do the work Doers focus on understanding what is expected of them and learning new skills...look to the future Leaders must get new things started and then step back to let others take the reins...productive culture and to correct systemic problems. Understanding these three roles allows you to identify what...the requirements of the current task. Most of us start as doers, some become managers and some take on ...

... Fulbright Visiting Scholar at the Pennsylvania State University. Imagine you are dealing with a defective...They first created a defective chloramphenicol resistance gene (CamR) by introducing a point mutation (... adenine base editor would restore antibiotic resistance. To find such a protein, they created a mutant...systems. Thus, the Yang Lab at The Pennsylvania State University (PSU) is adapting and improving base ...developed plant adenine base editor (ABE) vectors to install A>G or T>C mutations in the plant genome. We constructed...     These binary vectors could be used to generate stable genome edited plants via Agrobacterium-mediated... on the presence of an ‘NGG’ PAM at a suitable distance from the base (C/A) to be edited. But does this...

... laboratory tool often employed to establish cell lines that stably express a gene of interest. While ...background of the lines you are using, it is best to start from scratch. Obtain a vial of the desired cell ...production and infection.     Great transduction start with great virus If having happy cells is the first...extreme changes in osmotic pressure and pH can destabilize the viral envelope. One drawback of the multiple...The effect of freeze-thaw cycles on lentiviral stability depends on a variety of factors such as the transgene...al. found that lentivirus produced at pH 6 are resistant to multiple freeze thaw cycles. Consequently, ...prep!) and infect. While this approach is a great start to a successful infection, one point to consider...

...single cell isolation and downstream sequencing (Standage-Beier et al. 2019). TREE is a real-time, fluorescent...in emission spectra from BFP to GFP. Image from Standage-Beier et al., 2019. The team put TREE to the...reporter proteins. Protein translation requires the start codon of AUG immediately downstream of a kozak sequence...mScarlet reporter, luciferase reporter, and neomycin resistance reporter. Image adapted from Katti et al., 2020...generated a silent GFP construct, that contains an ACG start codon mutation, and integrated it into human and...As the initiation of protein translation at the start codon ATG is universal, the Dow lab successfully... including mScarlet-I, luciferase, antibiotic resistance markers, and other enzymes such as Cre-recombinase...

...new sample I always start by asking two questions: 1) Is the sample dynamic or static? 2) Is the sample ...acquired all fluorophores throughout the sample are constantly exposed to light, not just those in the focal...can a a high enough density of red-photons be establish for this to happen.Using red light has a second...within the depth of field of the objective (the distance in the axial dimension that will appear in focus... effects of high light doses to the cells. Thin static samples Ex: Fixed monolayers of cells or thin (... requirement for high temporal imaging speeds. Standard fluorescence widefield microscopy can be combined...require both optical sectioning, imaging over large distances and high temporal resolution. Traditionally, this...

...conclusion. Advice for Telling a Good Story Start at the start Any good story needs a solid point to kick...at. Whatever you’re working on, start wherever it makes sense to start and try to be as chronological ...almost all of us are programmed to appreciate and understand. We build narratives around the self, too — ...author. When I raised this, he was pretty angry and started arguing with me. First I calmed the situation down...for all of us.” This is a classic example of the STAR (Situation, Task, Action, Result) interview technique...and engage with and what parts you can leave out. Start viewing your work in the form of a story, and you...telling it. End at the end A story needs a good start point and it needs a good end point. One thematically...

...conformational states: bent-closed, extended-closed, and extended-open. In the two closed states, integrins...its open state, activating the receptor. Ligands can bind to integrins in their closed states (A) and ... ligands with high affinity. This extended-open state is key to strengthening ligand binding, mediating...in the extracellular environment. This further stabilizes the extended open integrin conformation. During...B) but with much lower affinity than their open states (C). Figure courtesy of IPI. IPI anti-integrin...rat or mouse variable regions fused with rabbit constant domains. All bind specific integrin alpha subunits...recommended for use in flow cytometry. Based on the established applications of the original hybridoma monoclonals...

...post-translational modifications, identifies a staggering ~250,000 phosphorylation events in the proteomes...proteomes of higher mammals (2). How can we begin to understand the importance of any of these phosphorylation...not reversible, and thus cannot reflect the true state of protein modification within the context of its...difficulties with kinase specificity in vitro. The establishment of a system in which purified, recombinant protein...provides researchers with a valuable tool for understanding the contribution of phosphorylation to enzyme...and second, through a gel shift assay using the PhosTag system (see below). This plasmid backbone can also..., one should optimize protein production using standard protein purification strategies; expression should...

...postdoc salaries as opposed to Staff Scientists Increase the Starting Salary for Postdocs to $50,000 ...symposium will prove incredibly important to the stability of the biological research enterprise going forward...need to know in order to even assess the current state of research became more clear throughout the various...information about the postdoc work force, problems start with the question of “What is a Post-doc?” The National...cost-effective for PI’s to pay postdocs as opposed to staff scientists. This results in a glut of postdoctoral... De-incentivize going into PhD programs as the standard option for scientists by requiring graduate students...$50,000 (the current median postdoc starting salary as reported by Paula Stephan is $40,000) Increase Knowledge...

...contributed by guest blogger Joachim Goedart, an assistant professor at the Section of Molecular Cytology...interference is known as steric hindrance. For instance, GFP may occlude catalytic sites or obstruct binding...Organized Smooth Endoplasmic Reticulum (OSER) assay (Costantini et al., 2012) measures homodimerization of FPs...This assay is quantitative and is currently the standard for assessing oligomerization in cells. In addition...protein characteristics such as the brightness, photostability, maturation time, and acid sensitivity of various...parts of the fusion from N- to C-terminus. For instance, Lifeact-mTurquoise2 (Plasmid #36201) or mScarlet-tubulin...blogger, Joachim Goedhart! Joachim Goedhart is an assistant professor at the Section of Molecular Cytology...

...feelings, low morale, poor decision making, and stalled projects. You want to identify and address these...also be categorized as either “personal” or “substantive”. A personality-based conflict occurs when two...a lab or work environment if left unchecked. Substantive conflict occurs when people or teams who normally...”) when in fact many sources of conflict are substantive (“Person C told Person A one thing and inadvertently...in my current role revolve around missed tasks, stalled projects, and disagreements over prioritization...through multiple channels is not reasonable or sustainable. That said, when you know that a person or team...can indicate confusion around... Ownership: Misunderstandings about who is responsible for what tasks or...

...Macaques N/A Stanton et al., 2023 AAV-MDV1A CNS Mice No (LY6C1) Stanton et al., 2023 ...The blood-brain-barrier (BBB) exists to prevent substances in the blood, like proteins and viruses, from...into the brain. While helpful from a biological standpoint, it makes delivering AAVs to the brain difficult...interest, and health. While it’s always helpful to start with a literature search to see what others have...considerations you’ll need to be aware of before starting an experiment. Controlling expression As systemic...sensors, CRISPR elements, etc... *These are only starting recommendations; you will still need to experimentally...are a good fit for your experiment, it’s time to start selecting and testing systemic capsids! Figure 2...

...Kostman.   Important considerations before you start an experiment with CRISPR The hammer, the jigsaw... an alternative ATG downstream of the annotated start codon. Likewise, we avoid target sites that code...undertaken lightly! Indeed, truly achieving the gold standard requires not one but two rounds of single cell...in a 5 - 10 nt window relative to the PAM, and bystander edits are possible if there is another target ...target a ~100nt window upstream of the transcription start site (TSS), while for CRISPRi, a ~100nt window downstream...the target (e.g. accessibility due to chromatin status). No computational prediction is ever perfect, ...nevertheless still lead to activity has been established, and can be used to identify sites that are likely...