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Toeprinting maps a reverse-transcription stop caused by an assembled ribosome or initiation complex on RNA. It can report occupancy near a biological translation start site, but controls are needed for stops caused by RNA structure or other bound proteins.
Dynamic light scattering analyses fluctuations in scattered light to infer diffusion and hydrodynamic size under a suitable model. Large particles can dominate the intensity, making it sensitive to aggregation but limiting simple interpretation as a number distribution.
Isothermal titration calorimetry measures heat accompanying additions of one binding partner to another at controlled temperature. With suitable concentration ranges, stoichiometry and a binding model, it can estimate affinity and binding enthalpy; dilution and buffer effects need controls.
Surface plasmon resonance can monitor binding near an optical sensor surface in real time through refractive-index changes. Concentration-dependent association and dissociation can constrain kinetics, subject to controls for nonspecific binding, transport limitation and multivalency.
A screening assay measures candidate variants individually or in distinguishable compartments. In protein engineering, expression, stability and intrinsic activity must be separated when interpreting an increased signal.
A selection assay preferentially retains, amplifies or permits survival of candidates satisfying a criterion. It differs from directly measuring every candidate and can fail if the selectable phenotype becomes detached from the intended biochemical function.
Electron cryotomography reconstructs three-dimensional electron-scattering density from a tilt series of a vitrified specimen. It can reveal native cellular assemblies such as receptor arrays, subject to dose, sampling and resolution limits.
traction force microscopy estimates forces that cells exert on a deformable substrate from measured substrate displacement and a mechanical model. Calibration, boundary conditions and material properties affect the inferred forces.
Introducing selected isotopes into molecules to support detection or assignment. In nuclear magnetic resonance, labelling can add observable spins or suppress unwanted relaxation pathways.
A repeated peptide-epitope system detectable by fluorescent binders. Placing tags on nascent chains can make a biological translation site visible separately from completed proteins.
Detection of selected genomic regions with complementary fluorescent probes, supporting spatial-distance and nuclear-position measurements. Fixation, denaturation and probe design can affect the measurement.
An engineered transcript containing a selected RNA splicing region in a controlled expression context. Mutating a candidate cis-regulatory element tests local function, but an isolated construct can omit distant regulation or native chromatin context.
Experimental inference of RNA secondary structure or accessibility from chemical or enzymatic reactivity. Changes in reactivity can also reflect protein shielding, so comparisons and orthogonal controls are necessary.
Sequencing of RNA fragments protected by ribosomes to measure their positions on transcripts. Occupancy measures a combination of entry, passage and dwell time; more footprints can reflect slower elongation rather than more completed protein.
Pinned article: Introduction to the OurBigBook Project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
Intro to OurBigBook
. Source. We have two killer features:
- topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculusArticles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
Figure 1. Screenshot of the "Derivative" topic page. View it live at: ourbigbook.com/go/topic/derivativeVideo 2. OurBigBook Web topics demo. Source. - local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 2. You can publish local OurBigBook lightweight markup files to either OurBigBook.com or as a static website.
Figure 3. Visual Studio Code extension installation.
Figure 5. . You can also edit articles on the Web editor without installing anything locally. Video 3. Edit locally and publish demo. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension. 
- Infinitely deep tables of contents:
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact