Hot (biochemistry-related) topics

Updated 31/01/2017

I am in charge of a module entitled “Advanced Skills for Biochemistry“. Our third year Biochemistry (Honours) students take this course. One of their tasks is to prepare and present a poster on a hot topic or technique. I have therefore asked the world (via Twitter) and my colleagues at the Institute of Integrative Biology to come up with suggestions of topics for these posters, as well as references that students could use as a starting point.

  1. Genome editing with CRISPR/Cas9, suggested by Jerry Turnbull, Dada Pisconti and Pat Eyers:  perhaps this is a useful guide paper for its potential in a disease: ‘Prevention of muscular dystrophy in mice by CRISPR/Cas9-mediated editing of germline DNA.’
  2. Cellular Thermal Stability Assay (CETSA) for drug target identification, suggested by Pat Eyers: good starting points are: The cellular thermal shift assay for evaluating drug target interactions in cells and Monitoring drug target engagement in cells and tissues using the cellular thermal shift assay.
  3. Quantification of proteins in organisms, suggested by Pat Eyers; e.g. recent publication from here on ‘Direct and absolute quantificaion of over 1800 Yeast proteins via Selected Reaction Monitoring‘.
  4. Amyloid diseases (in this case Alzheimer’s disease) are possibly transmissible, suggested by Hannah Davies: the paper and some commentary articles and media coverage. [also some comments at PubPeer ; added by RL]
  5. Parkinson starts in the gut?  suggested by Jill Madine. Some media coverage.
  6. Lattice light sheet microscopy, suggested by David Stephens, from Bristol, via Twitter and by Violaine Sée; Betzig’s article.
  7. Ion mobility–mass spectrometry (IM-MS), suggested by Jerry Turnbull + relevant papers selected by Claire Eyers: Claire wrote a review on IM-MS and a research paper and she also points to this one from Carol Robinsons (Oxford)
  8. Selective Plane Illumination Microscopy (SPIM), suggested by Dave Mason; two good places to start with SPIM and some nice variants adding more planes.
  9. Open science, suggested by Dave Mason; application to big data in c elegans:
    cross over with SPIM (lots on the website: http://openspim.org/Publications )
    some nice discussion of pros and cons (for genomics).
  10. Signalling controlled by frequency modulation, suggested by Violaine Sée, e.g. this article.
  11. Organoids cultures, suggested by Dada Pisconti, e.g. this review Modeling mouse and human development using organoid cultures
  12. Tissue clearing techniques for optical microscopy, suggested by Marco Marcello, exemple paper here.
  13. Predicting contacting residues, within and between proteins, purely from sequence information (large alignments), suggested  by Daniel Rigden . This allows fold prediction, prediction of modes of interaction and many other applications. Review + amazing papers on predicting complexes and structures for uncharacterised Pfam entries.
  14. The potential and challenges of using recombinant spider silk in biomedical applications, suggested by Roger Barraclough, e.gTo spin or not to spin: spider silk fibers and more, and, Controlled assembly: a prerequisite for the use of recombinant spider silk in regenerative medicine?
  15. CryoEM – suggested by Steve Royle via Twitter; advances in electron detectors and software has led to explosion of new fascinating structures. Pat Eyers agrees and provides these examples of CryoEM of the anaphase promoting complex.
  16. XFELs open a new era in structural chemical biology, suggested by Svetlana Antonyuk, with these two additional references.

Additional topics

  1. Dynamics of outer membranes in bacteria (completely discounts ‘lipid raft’ hypotheses) suggested by Marie Phelan.
  2. Mitochondrial Biochemistry and aging, suggested by Roger Barraclough, examples of papers: Declining NAD(+) induces a pseudohypoxic state disrupting nuclear-mitochondrial communication during aging [As spotted by the students, it turns out that this paper has a significant number of PubPeer comments…] and NAD+ deficiency in age-related mitochondrial dysfunction
  3. Any of the topics highlighted in this special issue (except those already in the list above); suggested by Violaine See.
  4. What’s Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism, suggested by Violaine See
  5. Chromatin Domains: The Unit of Chromosome Organization, suggested by Violaine See
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