Teaching

Hot topics in Biochemistry

Every year our 3rd year Biochemistry students have to produce posters on hot topics in Biochemistry. And every year I ask colleagues to contribute some ideas for this list of topics. You can find last year’s list here; as it is still pretty current, we will just extend it below. And you can contribute to this year’s list via Twitter or in the comments below.

#22

 

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Nanoparticles for imaging and sensing in biology

This is the title of a 3x1H45 course which I will give early September at the European School On Nanosciences and Nanotechnologies (ESONN) in Grenoble. The focus is on inorganic nanoparticles, e.g. gold, silver, iron oxide, quantum dots for biological applications. It will be the third year I give this course. It is a small class format with 21 students coming from all over the world, from New Zealand to South Africa, Denmark, Italy, India and France.

I have opted for a mostly discussion-based format centered around selected publications. I am asking readers of this blog (optional but very much welcome!) as well as students registered for the track B of ESONN15 (mandatory) to suggest at least one article for discussion. To suggest a paper, simply add a comment to this post with a reference (link to the paper would be even better).

Papers can be selected because they are historic landmarks in the field; or because they are recent ground breaking discoveries; or because they raise important questions that we need to discuss to move forward. Please provide one or two lines of justification for why you think we should discuss this paper.

Over to you!

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.
  17. Dynamics of outer membranes in bacteria (completely discounts ‘lipid raft’ hypotheses) suggested by Marie Phelan.
  18. 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
  19. Any of the topics highlighted in this special issue (except those already in the list above); suggested by Violaine See.
  20. What’s Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism, suggested by Violaine See
  21. Chromatin Domains: The Unit of Chromosome Organization, suggested by Violaine See

#socialmedia4academics

I ran today a one hour training session for researchers at the University of Liverpool about online presence. About 20 researchers from very different backgrounds (from language to physics, chemistry  ecology, etc) mostly at the post-doctoral level attended. We started with a round table where I asked each participants to tell which social media they use and what they expected from the workshop.

Many were Facebook users, mostly for personal networking, while a few had started to use it for professional networking too. Research Gate and LinkedIn were prominent as well (often with low level of usage). Google+ had one mention. One or two had limited experience of Twitter. One question that came several times was the personal versus professional limit. How much should we keep private? I don’t think there is any easy answer to this question, except that it is useful to understand how each tool you use work and therefore how to control what you are actually sharing or not. In that context, Facebook is a bit of a pain while Twitter is simple: everything is public so don’t share what you want to keep private.

Does it mean though that everything on your Twitter feed has to be serious professional stuff devoid of any personal aspect? I asked this question to Twitter during the event itself

Vladimir Teif responded immediately

I don’t actually agree with Vladimir (you can check my reply to him on Twitter), but thanks to him for this nice demonstration of the power of real-time conversation and crowdsourcing of  information.

When preparing this session, 12 hours before the event, I had asked on Twitter suggestions on of posts an points on social media for academics. I got a number of responses:

 

 

 

 

 

 

 

 

 

I ended up talking too much, mostly advertising the benefits of Twitter. Whether I have convinced them or not will be seen in the number of them that join and tweet me in 2015. Or participate in the comments section below. So far so good:

//platform.twitter.com/widgets.js

Interactive tools for teaching

I attended a teaching training session today. Here are the notes taken by Violaine Sée (who also attended). Feel free to suggest other tools in the comments below.

**********

1. Padlet: alternative to post it note, record of engagement, visual record. Sign up, then get a discussion wall. Can be used to get ideas floating from students, answering a question etc. Be careful they might want to post silly things.

Can be used to share resources for film making for example, and then people can add their own.

2. Todaysmeet
Backchannel chat platform.
Create a room either for single session or entire module.
Set guidelines before you start.
Useful to get fast feedback or questions during the lecture or end of the lecture.
Only micro messages. You can embed the link into vital, so the discussion is recorded.

3. Voicethread
On line discussion. Upload a document and then people can contribute. Good for peer assessment. Better for smaller discussion. Upload their videos. Others can make Audio or text comment at specific points in the video. Need to register for posting. Can only post 5 items at a time for commenting (in the free version). Can be used to provide feedback?

Zaption: can upload YouTube videos and then allow for commenting.

4. Polleverywhere text wall
Good for obtaining thoughts and feeling of students. Multiple ways students can respond: web interface, text message Free account is limited to 40 responses.
Possible to display wall answers live but also nice word cloud representation of multiple answers.

Nanoparticles for imaging and sensing in biology

This is the title of a 3x1H45 course which I will give early September at the European School On Nanosciences and Nanotechnologies (ESONN) in Grenoble. The focus is on inorganic nanoparticles, e.g. gold, silver, iron oxide, quantum dots. It will be the second year I give this course.

I have opted for a mostly discussion-based format centered around selected publications. Last year, I chose the publications and distributed them during the lectures, but let’s try to get more organised.

I am asking readers of this blog (optional but very much welcome!) as well as students registered for the track B of ESONN15 (mandatory: deadline Friday 28th August) to suggest at least one article for discussion (depending on the success of this crowd sourcing effort, we might or might not be able to discuss all articles). To suggest a paper, simply add a comment to this post with a reference (link to the paper would be even better).

Papers can be selected because they are historic landmarks in the field; or because they are recent ground breaking discoveries; or because they raise important questions that we need to discuss to move forward. One line justification for selecting the paper would be great.

Over to you!

European School On Nanosciences & Nanotechnologies #ESONN2015

Applications are open for the European School On Nanosciences & Nanotechnologies, Grenoble, August 23rd September 12th, 2015. I will be one of the lecturers in session B.

ESONN 2015 (12th edition) is a three-week course aimed at providing training for graduate students, post-doctoral and junior scientists in the field of nanosciences and nanotechnologies. The academic and practical courses will cover aspects such as the elaboration, characterization and functionalities of nano-objects.

You can download the poster as a pdf here.

esonn2015