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Construction of a genetic toggle switch in Escherichia coli by Timothy S. Gardner and others by
Codex 0 2026-11-05
Primary source: www.nature.com/articles/35002131
Verified locator: Nature 403, 339–342, published 20 January 2000, DOI 10.1038/35002131. Primary indexed publisher title/byline: Timothy S. Gardner, Charles R. Cantor and James J. Collins. Abstract verifies synthetic bistability in E. coli and transient chemical or thermal switching.
Additional full-text verification: bioinformatics.cs.vt.edu/~murali/teaching/2003-fall-cs6104/papers/designer/gardner-nature-vol403-genetic-toggle.pdf reproduces the original Nature 403, 339–342 paper. Figure 5 (p. 341) shows individual-cell GFP expression distributions near the switching threshold. Methods, Assay of gene expression (p. 342), identifies the FACSCalibur flow cytometer, 488 nm excitation and 515–545 nm emission filter; Figure 6 distinguishes switching-time observations.
University of Colorado Boulder Parker Research Group primary alumni directory. Grad Students section, Daniela Teixeira entry, records training2001–2005.
September2003 institutional bulletin, PDF page9: laboratory photograph caption identifies Roy Parker in the foreground and colleague Ujwal Sheth. Photograph credit Jeff Topping. The accompanying research account discusses the yeast mRNA-decay investigation. The photograph remains externally hosted.
Processing bodies require RNA for assembly and contain nontranslating mRNAs by Daniela Teixeira and others by
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RNA11,371–382(2005), DOI10.1261/rna.7258505. Primary byline Daniela Teixeira, Ujwal Sheth, Marco A. Valencia-Sanchez, Muriel Brengues and Roy Parker. Abstract: RNA dependence, stress responses and contrasting effects of translation-initiation versus elongation inhibition. Figure6 and associated Results: RNaseA treatment of enriched P-body fractions. Primary archive pmc.ncbi.nlm.nih.gov/articles/PMC1370727/ .
Primary source: mrclmb.ac.uk/news-events/articles/chris-oubridge-1966-2020/
Verified locator: Institutional primary obituary headed Chris Oubridge(1966-2020); opening states death25August2020. Research account identifies U1A/RNA recognition and subsequent spliceosome studies. Named photograph directly linked from the page. Original1994 publisher byline independently verifies Chris Oubridge for DOI10.1038/372432a0.
Official BioFrontiers profile, research on eukaryotic mRNA biogenesis/translation/degradation, affiliations and portrait. Institutional CV experts.colorado.edu/vitas/151440.pdf p.1 confirms 1985 UCSF doctorate; p.3 publication6 identifies the original1987 U2 study. Accessed2026-11-03; original Roy Parker title retained without middle-name expansion.
Decapping and Decay of Messenger RNA Occur in Cytoplasmic Processing Bodies by Ujwal Sheth and Roy Parker by
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Science300(5620),805–808(2003), DOI10.1126/science.1082320. Full primary bylines Ujwal Sheth and Roy Parker. Abstract and Figures1–2: functional fluorescent protein fusions localize decay factors; decay-pathway perturbations change foci; decay intermediates localize to these bodies. These observations support localized processing without proving every visible focus is required for all mRNA decay.
Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin by C. Oubridge and others by
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Nature372(6505),432–438(1994), DOI10.1038/372432a0. Indexed primary title and byline C.Oubridge, N.Ito, P.R.Evans, C.H.Teo, K.Nagai verify a1.92angstrom RNA-binding-domain/RNA-hairpin crystal structure. Title preserves published A spelling for angstrom. The source heading retains the abbreviated first-author byline. Publisher endpoint www.nature.com/articles/372432a0 was inaccessible; no unverified atom-contact or kinetic constants attributed to it. Existing2009 U1-core paper independently supplies U1A placement at U1 stem-loopII and the distinction between core crystallization and a complete-particle model.
The indexed original publisher record explicitly identifies the first author as Chris Oubridge. Its abstract specifies a21-nucleotide RNA hairpin,ten-nucleotide loop and1.92Å structure,including loop contacts at the protein beta-sheet surface. The primary indexed byline and named MRC obituary now establish the fuller identity; direct publisher open still redirects to an inaccessible identity endpoint. www.nature.com/articles/372432a0
Official Department of Microbiology and Cell Biology profile: Umesh Varshney (IISc Honorary Professor); Research, Protein Synthesis and DNA Repair sections identify research areas and model systems. First faculty image immediately accompanies his profile. Accessed2026-11-03; no inferred birth date, biography dates or awards.
Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA by Roy Parker and others by
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Cell49(2),229–239(1987), DOI10.1016/0092-8674(87)90564-2; PMID3552247. Indexed byline R. Parker, P. G. Siliciano, C. Guthrie. Abstract: two branch-site mutants in an actin-HIS4 fusion, predicted compensating U2 changes and allele-specific biological/biochemical suppression. Full first-author identity verified by Roy Parker’s institutional CV experts.colorado.edu/vitas/151440.pdf , p.1 name and p.3 publication6, also the official laboratory publication list www.colorado.edu/lab/parkergroup/publications (1987). Other indexed initials remain unexpanded.
Mutants of initiator tRNA that function both as initiators and elongators by Umesh Varshney and others by
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Journal of Biological Chemistry 266(27), 18018–18024 (1991), DOI 10.1016/S0021-9258(18)55231-5. Indexed byline U. Varshney, C. P. Lee, B. L. Seong, U. L. RajBhandary. Original first-page byline reads Umesh Varshney, Chan Ping Lee, Baik L. Seong and Uttam L. RajBhandary in the indexed original PDF citeseerx.ist.psu.edu/document?doi=c871e93e20447352f0f2e44bfca24f5146d4821a&repid=rep1&type=pdf . Abstract: acceptor-stem and anticodon variants, amber suppression, and one mutant acting at upstream and downstream UAG codons. Full PDF fetch returned cache miss; original indexed first page and primary indexed abstract verified.
Official laboratory biography, “Short biography”: 2007 undergraduate degree, 2013 doctorate on pre-mRNA splicing catalysis, 2014 move to structural postdoctoral work, and 2020 fellowship. Companion departmental profile www.bioch.ox.ac.uk/node/1889921 identifies the same scientist and labels its portrait Sebastian Fica. Checked 2026-11-03; no middle-name expansion or inferred birth date.
Crystal structure of human spliceosomal U1 snRNP at 5.5 Å resolution by Daniel A. Pomeranz Krummel and others by
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Nature458(7237),475–480(2009), DOI10.1038/nature07851; PMID19325628. Primary first-author byline Daniel A.Pomeranz Krummel verified. Abstract, Structure determination and Figures1–4: reconstituted U1 functional core, seven Sm proteins, heavy-atom labeling and 5.5angstrom map. Engineered/truncated particle lacks U1A; Figure5 adds the known U1A–RNA structure to model a complete particle. The crystallographic core must not be described as every component of an intact native U1 particle.
Escherichia coli formylmethionine tRNA: mutations in GGGCCC sequence conserved in anticodon stem of initiator tRNAs affect initiation of protein synthesis and conformation of anticodon loop by B. L. Seong and U. L. RajBhandary by
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PNAS 84(2), 334–338 (1987), DOI 10.1073/pnas.84.2.334. Primary indexed abstract and initial-only bylines B L Seong and U L RajBhandary verified; no expansion inferred. Anticodon-stem substitutions followed by purification, aminoacylation/formylation, AUG-dependent ribosomal P-site binding, initiation-factor binding and in-vitro protein-synthesis measurements. Full-text repository: pmc.ncbi.nlm.nih.gov/articles/PMC304201/ .
Nature 503, 229–234 (2013), DOI 10.1038/nature12734. Author-hosted original PDF: full first-author byline Sebastian M. Fica, page 229; co-first-author contribution marked. Abstract and Figures 1–3: sulfur substitution/metal rescue in assembled yeast spliceosomes identifies U6 ligands positioning catalytic metals during both splicing reactions. No claim of protein-free splicing by the intact cellular machinery.
A compensatory base change in U1 snRNA suppresses a 5′ splice site mutation by Y. Zhuang and A. M. Weiner by
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Original experimental article, Cell46(6),827–835(1986), DOI10.1016/0092-8674(86)90064-4. Institutional primary abstract: co-transfection of mutant adenovirus E1A and human U1 genes, efficient rescue at donor position+5 but weak rescue at another site position+3; base pairing necessary but insufficient. Published initials retained; no expansion of Weiner identity inferred.
The Medicago genome provides insight into the evolution of rhizobial symbioses by Nevin D. Young and others by
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Nature 480, 520–524 (2011), DOI 10.1038/nature10625. Primary byline Nevin D Young verified. Abstract and Figures 1–3: legume model, draft genome assembly, duplicated genomic regions and nodule-enhanced gene comparisons. Full text pmc.ncbi.nlm.nih.gov/articles/PMC3272368/ . No expansion of the middle initial or inferred personal dates.
Circular RNAs are abundant, conserved, and associated with ALU repeats by William R. Jeck and others by
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RNA19(2),141–157(2013), DOI10.1261/rna.035667.112. First-author full byline William R Jeck verified. Abstract and Figures1–4: RNA sequencing with/without RNaseR, enrichment of backsplice junctions and complementary validation. Study-level support for many endogenous circular RNAs, not a universal claim that every resistant transcript is circular or that all circular RNAs are noncoding.
Independent functions of viral protein and nucleic acid in growth of bacteriophage by A. D. Hershey and Martha Chase by
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Journal of General Physiology36(1),39–56(1952); DOI10.1085/jgp.36.1.39. Original byline A.D.Hershey and Martha Chase retained. University-hosted original scan www.mun.ca/biology/scarr/Hershey_%26_Chase_1952_J_Gen_Physiol_36%2C39-56.pdf ; primary indexed text pp.50–53, including p.52: Waring-blender stripping, centrifugation of extracellular sulfur label and comparison of transfer to progeny. The scanned PDF opens but text extraction is limited; precise indexed primary passages and original abstract used. No full-name inference from Hershey initials.
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





