Teaching

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.

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

#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

#LearnIT: Blog it! Tweet It! Film It! Wiki It!

That was the name of a staff-student exchange forum which I attended earlier this week. Georgina Turner wrote a blog post on the event at the Digi Learn Blog.

My impression is that there are plenty of exciting opportunities to use social media in teaching but that we have not yet seen the take off. The barriers seem to be more cultural, for both staff and student, than technical. While I am looking forward to the 10 days of Twitter at the University of Liverpool (particularly the last three days as I am already a regular Twitter user), setting up a Twitter account, a YouTube channel or a blog does not require any particular advanced technical skills. It requires a desire to engage and experiment with these tools. There are plenty of open resources to help.

The few things I picked up from the workshop because they resonate with my experience or things I want to do:

  • Students blog/videos etc: open platform or closed? As mentioned by Georgina, we heard from Dr Ian Walkington, and one of his students, Alistair Craig. Ian had asked students to create some videos about climate change (with an engineering angle; I don’t have the exact topic at hand – nor the videos…). They both emphasized that the exercise was an excuse to learn about an academic topic as well as learning how to use efficiently modern communication tools. Ian had made the decision to keep the videos private, i.e. hosted on our University VITAL platform, rather than say YouTube. Alistair seemed to regret that choice and I tend to agree with him that publishing those videos and sharing them more widely would be beneficial for everybody. A great example is the work of @Prof_Dave and his first year Chemistry student video channel. This experiment is further discussed in iTube, YouTube, WeTube: Social Media Videos in Chemistry Education and Outreach, J. Chem. Educ., 2014, 91 (10), pp 1594–1599. We are planning to do something similar for our Biochemistry students from next year as part of a third year module.
  • Georgina mentioned the use of Twitter walls to make lectures to large groups interactive. Sounds like a good idea which I might also experiment next year within another module (quantitative skills to first year biology students where I teach to about ~300 students). I have experimented with Polls Everywhere with some success but Twitter walls offer different possibilities. Georgina mentioned technical difficulties but it looks like our support team has this in hands.

Not discussed in the workshop, but something I have started experimenting with this year and I am very keen to push further in the years to come, is the use of open science notebooks for scientific research projects such as our Honours projects. Gemma Carolan (3rd year student), with the support of Dave Mason, image analyst in our Centre for Cell Imaging (and also new blogger) is currently live publishing her results here. Through this process, students would learn about the benefits of open science, get feedback on their work potentially from scientists around the world, disseminate their research, and also improve their digital literacy skills.