Tuesday Meeting?

Hi all,

Ross says that 20th November should be possible for the exam - he says he can start us off at 10 (and have the exam run 10am - 12pm). Is this still ok for everyone?

Also - do we still want to have a session on Tuesday? If so, maybe we should do any of the marking and peer evaluation things that we still have left to do and bring them on Tuesday so we can get all the rest of the assessment except for the exam all finished up and finalised.

Kristen

Late post for presenting topic...

Hi guys, sorry I am posting this so late... I forgot last night :S Am really really tired, so we'll see how the presentation goes. Nevertheless, the topic is a cool G-protein, which has been biophysically analysed. Its awesome. The paper is "Biophysical Analysis of the Interaction of Rab6a GTPase with Its Effector Domains."

Also, sorry I haven't found a paper for discussion time this week yet... so, to be continued I guess.

Alex.

The rules of disorder or why disorder rules

Hi everyone,

Apologies for not posting this sooner. The paper I have chosen for this week is called "The rules of disorder or why disorder rules". It focuses on a group of proteins found in eukaryotic cells that don't have a unique three-dimensional structure, but are still functional. These proteins adopt different folds when they interact with different partners - so in essence, their function defines the structure of the protein.

I'd never heard of these kind of proteins before, so was interested to learn something more. The paper itself doesn't focus on just one protein, but gives a few different examples.

See you all at the session!

(Also - at Tomas, who I'm assuming has done up the poll that has appeared - I can't possibly answer a question that asks two questions in one with only one poll option! Have two polls for two questions :P )

Structure, Property and Function, Relationships

Hey all,

I got some exciting news on the weekend. I have been offered a rural scholar ship at Griffith gold coast ^_^ which was my first preference. I'm quite pleased but not have 101 little practical details to work out.

For this weeks discussion topic I wasn't particularly clear on what direction we were taking the "structure, property, function relationships" topic (although our discussions often seem to choose their own direction on the day anyway :P). I cant remember if we were thinking proteins in particular or anything that fits under that heading such as cell shape and structure and their specific function.

Either way the paper I have chosen for for this week is on a protein which is a transcription inhibitor in barley but its general structure is found in many plants. Its expression in barley results in inhibition of growth of two side seed spikes which apparently makes self seeding of the plant more successfull. If this gene is removed however crop yield is tripled but the head are fatter and well likely to successfully self seed. This high yield barley is not a new thing and has been found to be used around the world in different cultures, most of which discovered it by selective breeding.

Diamagnetic levitation of biological organisms

Either nobody knows, cares or had the time to answer the question posed in the previous post, so I'll do it here:

More diamagnetic levitation movies...

The 'disproof' of magnetic levitation only applies for static charges. This video gives a quick demo of how you can test this yourself (I've never heard the audio track, so don't know if it's any good).

If you have a big enough magnetic field for its ρ/χ, you can levitate pretty much any living thing. Armed with this knowledge, biophysicists can conduct useful research like this and this.

On the Nature of the Molecular Forces which Regulate the Constitution of the Luminiferous Ether

What is photophysics without light, and how would light propagate without the luminiferous ether? Yes indeed, I finally was able to find a copy of this most excellent publication.

Ten points awarded if you can link the below to something we were discussing last week; twenty if you find a video of it and link it here.

Assessment

Does anybody know when exactly all of our outstanding/in progress assessment is due? Or what it is exactly? The online course profile doesn't seem to match with the notes I've taken down. Here's what me may (or may not) have left, not counting the exam and attendance next week:

• Report : According to the course profile, due on the 5th of November 2009
  
• Weblog : When do posts cease to 'count'? Next Tuesday, SwotVac, when the report is due or when the exam is held (for revision posts)? Anything after that is probably just for old time's sake..
  
• Peer evaluation : Will we be doing this next week during our usual meeting?
  

To me, it seems like some of the fine chronological detail have been lost in the background noise towards back end of semester (though this could be bias from looking at the video on this site while trying to get slides today), or my note-taking during the first couple of weeks wasn't so good. Can anybody confirm any deadlines for me please?

Edit: cut mention of canned assessment item

Photophysics and coral reefs

This is the paper that I brought in today:
Wild, FJ; Jones, AC; Tudhope, AW:Investigation of luminescent banding in solid coral: the contribution of phosphorescence (2000).Coral Reefs 19:2, pp132—140.

I tried to find a good picture to answer Kristen's question about what the bands actually are (sorry for not getting around to it before we all left!), and I came across this excellent page from the Australian Antarctic Division's website. Look at the third picture on the page!

Ack: Try searching for trees rings photophysics, and see if it's as cool as coral..

The "Brainbow Mouse" - Don't cut the green fluorescent wire!

I can't resist tying this week to last. Follow the link and find out what the "Brainbow Mouse" is: http://www.nature.com/nature/journal/v450/n7166/full/nature06293.html

Ever see those old action TV shows where the hero has to diffuse a bomb? He calls his friend and his friend says something like "whatever you do, don't cut the green wire!". Well, what if the wires were all the same color? Poor hero!

This is exactly the problem that neuroscientists have had for years - how to figure out what connects to what when everything looks the same. This problem was addressed in the article by combinatorially expressing fluorescent proteins in mouse neural tissue. There are just a few FPs used, but each cell expresses the set in different proportion, allowing (I think) more than a hundred visually identifiable colors! Check out some of the pictures - they're more colorful than a hippie van...

"Killer Red" - The Fluorescent Protein that BURNS

This was going to be a comment on Alex's post about photosensitizers, but I thought I'd elevate it to a full post because its interesting...

Like photodynamic therapy AND fluorescent proteins, and want to put them together? Well, now you can!

Killer Red is a variant of a red FP from coral (maybe sea anenome?). It has been optimized specifically to spew out reactive oxygen species upon irradiation. Any organism which expresses this protein is born to BURN, BABY BURN!

Here's the link: http://www.nature.com/nbt/journal/v24/n1/abs/nbt1175.html Check it out!

PE surfaces & photophysics

Just a quick video I found. I wish I knew how to download it to bring it to class to discuss.
It's a graphic representation of radiationless decay. It shows a molecule switching seemingly effortlessly from an excited state to the ground state at the conical intersection of the two relevant potential energy surfaces for that molecule.
hopefully the link works! If not, here's the url: http://wavepacket.sourceforge.net/Demos/ConicalInter/Linear/2/surface.mpg

Photodynamic Therapy - Light for Treatment of Disease

I am personally fond of the fluorescent proteins and their applications to biological investigation, including FRET, however I decided that other papers for tomorrow had this area pretty well covered. So I embarked on a search for further photophysical applications in biology with relevance. I found many interesting papers, however many I felt were too specific in their study of obscure molecules to perhaps be relevant for a broad discussion, or results felt incomplete as investigation continues in the field.

Finally, I found what I consider to be a well rounded review of a topic with very important medical applications, Photodynamic Therapy (PDT). You may be familiar with the concept however it is new to me, and this paper ("Photophysics and photochemistry of photodynamic therapy: fundamental aspects") presents a clear photophysical description of the process.

If you are not familiar with PDT, it is used as a treatment for cancer and other diseases by specifically targeting and destroying unwanted/harmful cells. A light sensitive drug is administered that, upon absorption of light at the appropriate wavelength, essentially oxidises intracellular molecules, thereby destroying the targeted cells. An optical window for PDT in tissue is defined by the absorption spectra of the most important chromophores: water, hemoglobin, melanin, and cytochromes.

I look forward to a discussion of photophysics tomorrow. On another note however, I will be unable to attend for the second half of our meeting so perhaps the presentations (Ack and Tomas) could be in the first half? As a result I may have limited input in the following discussion. Regardless, see you all tomorrow. Cheers, Alex.

FRET efficiency between a mutant of whttp://www.blogger.com/img/blank.gtGFP (donor) & a newish red fluorescing derivative of DsRed, mCherry (acceptor)

hello.
My photophysics reading for this week has been "Quantitative FRET Analysis With the E⁰GFP-mCherry Fluorescent Protein Pair", published in August '08 in Photochemistry and Photobiology 85(1). I had trouble accessing the pdf via the library site, but the html option worked just fine.

In this article, some scientists from various institutions within the Scuola Normale Superiore in Pisa propose a new fluorescent protein pair (E0GFP-mCherry) which they argue is particularly useful for FRET experiments in living cells.

The link here to Kristen's paper should be obvious and, in case you're interested, I got a bit carried away trying to find a link to Michael's. I might have come up with a link that actually has some conceptual substance by Tuesday, but in the meantime here's my best effort: mCherry is a monomeric derivative of DsRed, a red fluorescing protein derived from stony coral. Michael's paper features HcRed, which is also red fluorescing and also derived from an anthozoa, but is dimeric & found in nature in an anemone, not a coral.

back on track... my article describes the quantitative determination of FRET efficiency for this pair using fluorescence lifetime imaging spectroscopy (FLIM) & acceptor photobleaching (APB). I found the format a bit "biology-esque" (with descriptions of method focussing on technique used for, say, cloning proteins) but these were all new ideas to me so it was interesting and I coped! I recommend skipping to the treatment of FLIM & APB in the Results section which was somehow more conceptual.

The authors also talk about "the recent phasor approach" to FLIM, which I had to go here to understand.

Rar-red Fluorescent Protein

Hey all, the paper I chose for this week is about the Far-red Fluorescent protein.

I came across it when looking for a paper on structural analysis of a protein (for a biochem subject) with the condition that it was co-authored by someone at UQ. Initially I looked at the first name from UQ which was Sean C. Smith and thought no idea who that is but who cares it fits the criteria. It wasn't untill today that I thought hey maybe that paper would have something interesting to talk about for biophys and had a second look at it. To my surprise the paper actually had two people listed as from UQ the second of which was "SETH OLSEN"! I'm not sure how I managed to miss that the first time.

The paper talks about both chromophores (organic molecules which can provide some of those vivid colours we see in plants and animals) and fluorescent proteins, both of which have a very similar structure with only a small conformational change providing their functional diversity.

The paper is:

The 2.1 A° Crystal Structure of the Far-red Fluorescent Protein HcRed: Inherent Conformational Flexibility of the Chromophore, J. Mol. Biol. (2005) 349, pg. 223–237.

Here is the abstract and I accessed the paper through the UQ library site.

Photophysics and GFP

Hi all,

A reminder that this week we're reading about photophysics. If everyone was able to post their reading on the blog as soon as possible that would be much appreciated - that way when we get to the tutorial we can discuss things that we found interesting about other people's papers, or things that we didn't understand.

This week I've chosen a paper about GFP (green fluorescent protein), for which the Nobel Prize in Chemistry was awarded last year for its discovery and development. The paper is titled 'Excited state reactions in fluorescent proteins' from Chem Soc. Rev., 2009, vol 38 p 2922- 2934 (If you're not at uni, you will be able to find the paper through the library or Web of Science).Whilst the paper at first glance appears to be a bit long, I think that the most interesting sections to us are the Introduction (which gives a good background) and section 3 - Photophysics and proton transfer in wtGFP. It turns out that the wild type version of GFP described in section 3 fluoresces much better than the chromophore of GFP on its own (described in section 2). Section 4 describes how things change when GFP is mutated, and section 5 is on 'second generation fluorescent proteins'. If you're running seriously short of time, I would at least recommend reading sections 1 (Introduction) and 3.

For those who aren't familiar with the terminology, 'quantum yield' essentially refers to the ratio of photons in to photons out. This is either expressed in percentages, or a decimal. A high quantum yield means that your molecule is very fluorescent and a high amount of light that goes in is converted into fluorescence. A low quantum yield means that most of the light that goes in decays non-radiatively, and most of the light energy is not re-emitted.

For those that are stuck as for where to look, some good examples of photophysics are molecules that use FRET, or the use of FRET to get information about your molecules of interest, biological molecules that fluoresce or absorb light, articles about the use of GFP (the one I have posted is mostly about energy transfer in the molecule itself) or in photosynthesis (I only discussed purple bacteria in my talk). Once you start looking, you should find lots of examples.

using neural networks to model recognition of handwriting

So after my usual bouts of indecision, here's my paper for tomorrow:
http://www.cs.utoronto.ca/~hinton/absps/ijcai05.pdf
Sorry to post it so late.

Apparently using neural networks to model handwriting recognition is not a very new thing, but:
1) it's new to me! i think this paper could make a nice link in our discussion between free energy minimisation and Michael's words on Bayesian theory.
2) this particular approach uses multiple neural networks to model the recognition of finer and finer details in handwriting. from what i understand, THIS is a bit new. also, there is a great Flash demo online. I just have to find it again and i'll post it up!

Chaotic Neural Networks = Thoughts and Actions

Hi all,

This week I found a paper that comes back to the idea of biological disorder leading to order. This is found in the sense that a novel system of mathematical/computational learning produces a systematic and coherent response from an initially chaotic state. The system is modeled with variables that represent neurons and synapses.

The title of the paper is "Generating Coherent Patterns of Activity from Chaotic Neural Networks"and I have posted a link to the paper (using Ross's method) here. The procedure is called FORCE learning and as expected there are a couple of large math equations, however I find the concept in general rather interesting and thought provoking.

See you all tomorrow.

Alex.

The Baffling Bayesian Brain

Hey I'm not sure if you guys covered this topic when you did mathematical biology, but Idid a section on how the brain is thought function according to Bayesian theory. If you havn't heard of Bayesian theory before don't stress its pretty easy and I'll do my best to summarise it tomorrow.

My neural networks reading for this week (which is a little bit of a tangent but I find it really cool so that justifies it in my mind :P) is an experimental paper I first saw in mathematical biology, which suggests that the brain may function on basic Bayesian theory.

The paper is: Bayesian integration in sensorimotor learning - Nature 427, 244-247 doi:10.1038/nature02169;

See you all tomorrow.

P.S I think my med interview went really well but its hard to know for sure.

This week's reading

Hi all,

Just a reminder to everyone that we're supposed to be posting our reading for the week on the blog so everyone else can have a look at it and so we have something to discuss at our meeting tomorrow. If someone else could post something before late tonight so that I have a chance to look at it before tomorrow that would be great.

Kristen

Micheal's Presentation

Hey all sorry this is a bit late. My presentation is planned for this Tuesday and the paper I'm reviewing is "Folding at the Speed Limit", a letter to nature from: Nature 423, 193-197 (8 May 2003) | doi:10.1038/nature01609. It's about the speeds at which proteins fold with time scales dependent on the size of the proteins in question.

This all said I am rather stressed at the moment as am trying to complete a computational physics assignment before tonight as well as preparing myself for my medical entry interview tomorrow and somewhere in the gaps preparing my presentation. I sadly I forgot I had all these things on when I agreed to do my presentation this week. Ross and Seth I was wondering if I needed to could I postpone my presentation to the last week where there is currently still a slot open? At the moment I would still like to do it this week and could probably do the finishing touches after my interview but I'm not really sure what sort of working state I will be in Monday night.

I will check the comments on this post for you responses and if need be I can make my presentation happen this week, I'm just worried I may not be able to put my best effort into it.

Kristen's Presentation

Hi all,

My presentation this Tuesday will be on "How Nature Harvests Sunlight", looking in particular at the light-harvesting apparatus of purple bacteria. The main article I have focused on is Hu, X. and Schulten, K (1997) 'How Nature Harvests Sunlight', Physics Today, August 1997, p28 - 34. The UQ library has access, so this can be found by doing a quick search of Web of Science (or similar), or I have posted a link here.

I don't want to get too focused on the tiny details, especially since I know that there are those of you who aren't altogether comfortable with lots of quantum mechanics, so I'll be sticking mostly to concepts (in other words, don't get freaked out).

Kristen

Neural Networks Introduction

I had a flick through the Biophysics textbook by Cotterill, which had a section on neural networks. Since we probably don't all have access to that particular book, I've done a summary of it and uploaded my summary here. It's pretty basic, but I thought it would be good background reading to get us started. Let me know if you have any problems with the file.

I tried to look for some of Steinbuch's original papers. Unfortunately, the UQ library doesn't seem to have access to a lot of them, and the ones that I did manage to view were all in German.

If I get the time, I'll try to post a relevant paper.

If there is anything confusing or that doesn't make sense in the summary, feel free to comment.

Advertising: PAIN Lab Tour

If you want a look-in at some of the labs in Physics and the IMB, consider coming along to PAIN this Friday for a quick lab tour. All interested will be meeting up at 5pm in the physics tearoom.

2 micron polystyrene spheres arranged to form the word `hi' using optical tweezers (Laser micromanipulation lab, Physics)

900 MHz (21.1 T) NMR Spectrometer (Institute for Molecular Biosciences)

Thermodynamics of Computation

This site provides a good, fairly accessable introduction to the thermodynamics of computation with links to other sources.

(Disclaimer: if you go to the about page, you'll find out why I know about this. And also why another of us may find this familiar..)

housekeeping from yesterday

Just the updated schedule we came up with yesterday:

week11: Neural Networks (everyone to find an article/site, post it on the blog and come to the tute prepared to explain it to/discuss it with others) / Kristen & Michael present

week12: Photophysics / Ack & Tomas present

week13: Structure, property, function relationships / Alex presents

And Ross's hot tips for inserting links to papers in our posts:

Type " dx.doi.org/10.10xx " , where 10.10xx is the digital object identifier number. Every paper has one, and you can find it written on the paper usually wherever the other citation details are (along the bottom of the page, or up top right).

2009 Nobel Prize in Medicine or Physiology

Today's prize announcement is worth reading since it involves some cool chemistry and biology.

Hey all i'm sure we are all thrilled to be back from our, not so "mid" semester, "break" from lectures (at a cost of doubling our workload for the week).

That said I was able to catch up on a little bit of sleep and fit in a small social life.

Sadly this post is not going to be filled with to much content from out text as I managed to leave at home when scrambling out the door for my 8am lecture. This means I wont be able to finish the last part of my reading before the discussion (even google couldn't find a pdf copy for me) but has meant I have time free to do some blogging.

I find the content in this chapter interesting but have come across the majority of the concepts before. This leaves me with calculations and proofs for the concepts for new material which I personally, don't find very stimulating. Ironically most of the applications which I often find more interesting are in the second half of the chapter.

I'm not sure if this is covered in the chapter but I'm a bit confused as to the relation between energy and so called "calculation". By this I mean is there a direct measurable energy cost for our brain creating/calculating information. Of course the process itself is taking energy but in a physical sense is this all being dispersed as an increase in the kinetic energy of the ions traveling across the membrane and a decrease in entropy as the gradient across the membrane is reduced. Does this come back to our earlier discussion of so called "high quality energy"?

Tried to google these ideas but was getting nowhere quick so I will probably have to refine my search. Anyway I just noticed the time so even though none or you will read this before it happens see u in 2 minutes! =P

Micheal.

This week

Welcome back!
I trust you had a good week with a break from lectures (n.b., I did not say holiday).
Tomorrow we will discuss the last chapter of Nelson. It is a great one.

Biological question: How can a leaky cable (e.g., a neuron) carry a sharp electrical signal over long distances?

Physical idea: Nonlinearity in the cell membrane's conductance turns the membrane into an excitable mdedium, which can transmit waves by continuously regenerating them.

On more mundane matters on tuesday I want to
-give you a TEVAL to complete
-pin you down on paper presentation topics
-remind you of the assessment details

Also, I will be away for the following 3 weeks, but Seth will attend the tuesday tutorials and talks.