What's on

What’s On: June

June was a busy month for us all as Chris decided to host a research day for us all out at Crewe Hall. The aim of this research day was to give everyone a chance to present their data so far and bounce ideas off the rest of the group. The meeting went very well for all concerned (even me, I know I’m just as shocked as you) and we all got a lot of great ideas out of it. Special thanks go to Chrystelle Egger and Raphael Pastorello for attending the meeting and to Christopher Exley for hosting (and paying for) the event.

The beautiful Crewe Hall.

That’s the introduction spiel out of the way; let’s get on to the individual members. Starting our most handsome, talented and most of all modest member, me.

Ian:  Well as I said earlier we’ve all been pretty busy preparing for the meeting, which took place on the 24th June. Most of my efforts were concentrated on finishing up experiments that needed finishing whilst planning out my future work. I have some interesting work with relation to how sample preparation affects silica deposits found, but if I said any more at this point I’d have to kill you.

Emma: After optimising the methodology for the quantification of particulate aluminium,Emma started several studies to determine the particle size profiles of both clinical and research based aluminium adjuvants. These studies will involve monitoring and analysing preparations from undiluted solutions through to their introduction into a biological medium mimicking that at the site of injection. It is hoped that this information will provide a picture of what happens to a vaccine preparation upon injection and subsequently the environment encountered by patrolling innate immune cells.

To date, Emma has obtained particle size profiles of both clinical and research aluminium adjuvants in vaccine preparations and biological media and is now working on characterising the charges associated with these materials.

Chris: What of the Aluminium King? Well in addition to organising the meeting in Crewe, Chris had a research meeting with Xabi Lopez (San Sebastian) and Dominique Costa (ENSCP, CHIMIE-PARISTECH) in San Sebastian during the first week of June (it’s so tough at the top).The idea behind the meeting was too put some meat on the bones of a number of computational studies on aluminium which are beginning to take shape between these computational groups and us at Keele.

Krista: Like most of us, Krista has spent this last month getting all data ready and presentable for the research day. In addition to that, she also handed in her first year progression report which I’m pleased to say has been passed, barring a few ethical complications (apparently a lab rat gladiator arena breaches a few rules, but we’re working through some loopholes now).

Whilst she waits on ethical approval for her in vivo studies, she is focusing on some in vitro work involving the formation of hydroxyaluminosilicates using the various mineral water varieties, of which she has now quantified the silicon/silicic acid contents. As well as this she hopes to simulate a gut environment to see how the different forms of silicon absorb through the synthetic gut wall, as well as analysing what would happen if aluminium was added to this solution.

Matt: Following on from his last update, Matt has now identified a suitable paraffin-embedding protocol utilising agar as a support medium that works consistently. The agar itself acts as a support medium, allowing for the introduction of small or fragile samples within its matrices. He has found that the careful monitoring of paraffin temperature during the infiltration phase and extensive optimisation of both the dehydration and clearing phases are vital to sectioning success. Further to this he has now also established a suitable de-waxing protocol that must be performed to remove the paraffin wax from the sections, allowing them to be stained. He has also recently prepared an agar-cell block and is in the process of identifying the sectioned cells within the agar-films.

And that’s us done for now, stay tuned for our next update which will be pretty soon because this one is late…personally I blame Chris.

 

What’s On Update: April & May

Long-time no see everyone. Apologies for the hiatus but we’ve been pretty busy over here so updating this page was put on the back burner. The group has a big meeting at the end of June where we will be presenting a lot of results. As a result of that, we all had to go and actually get some of these fabled results.

So what have we been up to? Well we’ll start with Lady Emma of Shardlow. After successfully optimising her methodology for the quantification of particulate aluminium, she has been conducting several studies to determine the particle size profiles of both clinical and research based aluminium adjuvants. Accumulating data in order to build these profiles will involve monitoring and analysing these preparations from undiluted solutions through to their introduction into a biological medium mimicking that at the site of injection. It is hoped that this information will provide a picture of what happens to a vaccine preparation upon injection and subsequently the environment encountered by patrolling innate immune cells.

To date she has also obtained particle size profiles of both clinical and research aluminium adjuvants in vaccine preparations and is now working on obtaining these profiles when adjuvants are exposed to biological media.

Sticking with the ladies of the group, let’s look at what new kid on the block, Krista Jones has been up to. This month she has been examining qualities of the mineral waters even further, looking at particle size distribution as well as silica content with PDMPO fluorescence method Krista has also been looking at the kinetics behind the molybdenum blue reaction she uses to quantify silicic acid content. The speed and intensity at which the yellow colour complex forms, relates directly to the concentration and silicon species present in the water. Other than that she informs me that she is still liaising with the hospital regarding ethical approval for her MS study although she is edging ever so closer to being able to initiate analysis on herself and her peers on their renal handling of silicon. Joy. Krista has also been looking at creating an artificial gut lining, using dialysis tubing to synthesise an environment from which she can calculate the absorption of silicon across the membrane  Finally, she has been investigating previous work done on renal handling, in efforts to establish any correlations and anomalies that may affect her research.

Moving on, we come to James Beardmore. James has studied his HAS-B solutions with GFAAS and the graphite furnace very much disagrees with what the particle sizer indicated with the filtered solutions for Al. As a result of this discrepancy, he now plans to investigate Si content to confirm that he definitely had produced HAS-B in the first place.

He has temporarily paused lab work, with the exception of instructing a new student in how to make various silicon solutions, to modify and run his computational simulations. He has had some issues getting them to produce "Marvin-esque" particle size distributions but hope to have this sorted by the time this is read by anyone on the "what's on" page. Some initial trial runs predicted HAS-A and HAS-B formation under differing conditions, but need refinement. The software also needs a little re-coding so that more information can be extracted from the simulations.

From one of our glorious post-docs to another, here comes the man, the legend, the god amongst men that is Matthew Mold. Matt’s recent efforts have focused upon the optimisation of a suitable paraffin-embedding protocol utilising agar as a support medium. In spite of his (and mine, but more on that later) efforts he has been finding that the agar-blocks won’t fully infiltrate with molten wax following the usual dehydration and clearing stages typically employed. Extending the amount of time and replenishing the dehydrating and clearing solutions more often has however vastly improved the infiltration of melted paraffin into the block. A novel piece of trickery on Mr Mold’s part has ensured that the blocks are maintained at a constant temperature during the infiltration process which has improved results dramatically. The protocol now consistently works for his control blocks containing aluminium compounds and infiltration through the entire agar block is now achievable. The next step is of course to introduce the actual cells he needs to section and to establish whether the same protocol works for these samples and whether they can be successfully sectioned and viewed using light microscopy. Finally Matt has also been attempting to optimise some positive aluminium controls but more work is needed to identify the deposited particles with confidence. His research efforts are now focused here and he hopes to report something positive on that front in his next update.  We’ll be holding him to that promise.

Here it is folks, the main event and the moment you’ve all been waiting for. Introducing the inter-continental champion of the office, Ian Stokes (aka me). Well for the most part I’ve been doing the same thing as Matt; trying to embed tissue in paraffin wax. Unlike Matt though, I’m trying to embed rather large pieces of plant tissue which has meant that we’ve had to use fairly different method. It has also taken forever to optimise this method as it takes a few days each time you try it. If it doesn’t work then it’s back to square one. However my latest efforts have proved to be a rousing success (and just in time too).

I’ve also been performing a couple of experiments relating to silicic acid’s behaviour within a plant. One has been looking at the difference between drying out samples before digest versus digesting the material wet. I can’t go into why this is important just yet, but we think it might well be. The other experiment I’ve been working on is a way to measure the transpiration rate of my plants. This experiment also has the secondary goal of tracking the silicon content in the nutrient solution, hopefully shedding more light on the rate of silicon uptake in plants. Finally I’ve been doing some work with aniline blue, staining for callose in rice tissue.

Well that’s all folks, join us again next time.

 

What’s On: February & March

Roll up, roll up one and all and see the newest wonder of the modern world, the Keele aluminium group what’s on page update. There will be a little about everyone’s work later on but the meat of this delicious update comes in the form of the Tenth Keele Meeting on Aluminium which happened back in February.

Held just outside of Winchester at the Norton Park Hotel, the Tenth Keele Meeting on Aluminium was entitled “Illuminating and Elucidating Aluminium’s Exposome: From Geochemistry to Neurochemistry, From Microbe to Man”. With 92 attendees from all over the world, this was without doubt one of the top 5 aluminium based conferences to happen this year.

All of us (Ian, Emma, Matt, James and Krista) produced posters for the conference, which are now all up in the Birchall centre if you feel like swinging by and having a look. In addition to this, James and Emma gave short presentations on their posters.

We also had a wealth of talks from many other attendees of the conference, a summary of which is available in the Keele meetings section of the website. I’d like to thank our chairs who headed each session; Tamas Kiss, Lubos Burovka, Paula Goncalves, David Chettle, Leon Kochian and of course Christopher Exley.‌‌

The meeting also saw the English language premier of The Age of Aluminium, a new documentary featuring Chris, as well as other conference attendees. This film by Bert Ehgartner was created to reveal the possible health consequences of living in an age of aluminium to the public. A link to the English version will be available as soon as possible.

So what else have we been up to in addition to eating fine food and drinking wine? Well Emma has been in the lab optimising her methodology for quantifying the aluminium in various adjuvant solutions. So far this has yielded two blanks and one partially successful experiment (you can’t win them all it seems). When optimised she hopes to use this methodology to quantify aluminium.

Meanwhile Matt has been focusing his research efforts into preliminary studies investigating the potential uptake of aluminium in human cell lines. The work is being performed to shed light on some of the uncertainties currently being raised in the field of aluminium adjuvants in vaccine preparations. His initial studies have involved the optimisation of an embedding protocol suitable for sectioning cells, allowing for their subsequent staining. He has since managed to prepare several control blocks that require sectioning and if these prove successful he will go on to prepare blocks containing varying concentrations of aluminium to act as positive controls. Together this approach should hopefully allow for the validation of the techniques being used. Matt’s initial efforts are now focusing on research methods that have been well-established by the group with some modifications based on recent findings within the literature.

In other Matt related news, he has his paper; Copper prevents amyloid-β1–42 from forming amyloid fibrils under near-physiological conditions in vitro, published in Nature Scientific Reports. Link here: http://www.nature.com/srep/2013/130213/srep01256/full/srep01256.html

As for myself, I’ve been finishing up my work on the sample group from my experiment in Slovenia. Thankfully all that is left to do is the sectioning of fixed samples. To this end I’ve been helping Matt get his sectioning station set up in our lab. In addition to this I’ve been having some problems with infections in my rice growth set-up, however fingers crossed that is sorted now and I can get the paddy field back up and running.

Krista has been carrying out multiple repeats of her work to ensure consistency and reproducibility of data as well as finalising Ethical Approval (I’m sure you all know how much fun that is) for her peer study titled, Renal Handling of Silicon. She has also initialised Ethical Approval for a further study with MS patients to continue work done by Prof Chris Exley in 2006, also regarding the renal handling of silicon. Yet more ethical approval fun. Silly Krista, should have worked with plants, no one cares about their ethics.

Moving on to James, he has been doing more particle-sizing on different solutions. We noticed one morning that the lab was suddenly extremely tidy, which turned out to be the result of a Beardmore cleaning rampage whilst he waited for his experiments to finish at the weekend. Apart from going all Monica from friends on us, Jame has been looking at HASB solutions and getting some bizarre results that he really needs investigate further. He isn’t sure if Marvin (our particle sizer) is seeing much of anything that floats around in HASB solutions, as it doesn't show ridiculously-big particles in the solutions, but the particles it does see all disappear when filtered at 0.1µm. This implies that a lot of the particles in the solutions, thoughout the pH ranges where particles are likely to exist, are too big for Marvin to see. Testing of the filtrate by GFAAS should shed more light on this behaviour. Additionally, he took zeta potential readings, which for some solutions indicated few or no charged species, whilst for other solutions, charge varied, correlating nicely with what he believes to be initial HAS-particle formation and later precipitation.

Saving the best till last, the boss man has been pretty busy as of late. In addition to organising the Keele Meeting on Aluminium, Chris also gave his inaugural lecture as a professor (pretty sure he’s been putting it off for a while now). He kept things pretty light on the science and high on the entertainment as he did a whistle stop tour of his life’s work. We even had a lovely group photo taken afterwards.

As a final note, a great friend of our group, Professor Peter Plesch died on March 5th aged 95. Peter was a constant feature in the Birchall Centre from its establishment in 1992 through to just a few years before his death. We all benefitted from his charm and his wisdom and we will miss him.

 

What’s On January

Time for another what’s on page update. I know I know, you can barely contain your excitement. As always we’ll start with me because I’m the best.

Well I’ve been having some fun using yet more strange and new equipment, this time in the form of the new micro SEM the geology boys have. I’ve had some very pretty images coming through from the SEM analysis of plant silica (see below), though now comes the fun bit, figuring out what they show.

 

I’ve also been working through older samples that needed analysing, digesting frozen plant samples to determine their total silica content. The past couple of weeks have been spent slaving over a hot computer to put my poster together for the 10th Keele Meeting on Aluminium (I’m not actually doing anything on aluminium, but don’t tell them that).

Ladies first, so let’s start with Emma. In collaboration with colleagues in Sweden, Emma have been researching the influence of both preparation and biological media upon the average particle size distributions of two research aluminium based adjuvants over time. The data has taken her a month to collect but has highlighted some very interesting trends. Ultimately, this data will enhance knowledge of the chemistry which occurs when adjuvants are introduced into a cellular model allowing a greater understanding of what may influence biological mechanisms. She has also been working on the compiling the abstract book for the Keele meeting and preparing her poster for presentation (which has now been printed off and I can tell you, it looks fantastic).

So that’s Emma done, now onto the newbie. Krista has been looking at Graphite furnace Atomic Absorption Spectroscopy to measure total silicon content in waters in comparison to the silicic acid content, previously quantified by the molybdenum blue method and UV-VIS spectroscopy. The results that she has seen so far are interesting in the respect that total silicon and silicic acid ratios differ substantially in certain water samples. As with all of us, she has been preparing for the 10th annual Keele Meeting by producing a poster on this experimental work (which is now finished and printed, so make sure to look out for it at the Keele meeting). She has also been liaising with a group of MS patients and in the process of applying for ethical approval, in efforts to initialise a group study into the renal handling of silicon and aluminium excretion.

So what has our newest post-doc been up to? Well I’ll leave this to Matt as well to be honest, he outranks me and who am I to rewrite his masterful words?

“Hi all, another update for the ‘what’s on’ pages has been prompted by Ian and out of fear of being engaged in some bizarre practice, here’s what I have been up to. With the viva fast approaching my preparations have become somewhat more intensive yet I have managed to trawl through the literature on the new and exciting filed of aluminium based adjuvants that I have become involved in. My interests are currently focused on the potential cellular localisation of aluminium in a model of an aluminium based adjuvant, immune-potentiated-response. I shall be presenting a poster of my findings at the 10th biannual Keele meeting on Aluminium being held at Winchester from the 23rd – 27th February 2013. The meeting promises to be the most engaging yet, giving host to a culmination of the world’s research effort on aluminium”

Edit: Fabulous stuff from Matthew Mold, PhD…….yes you heard me right, Matt has since passed his viva *cough*minor corrections *cough* and is now a bona fide doctor. Huzzah and all that jazz.

 

Finally we come to the esteemed Dr Beardmore. James has been doing some more design work and coding for his new detailed simulations, and has been doing some performance testing of different programming languages (FORTRAN, C and Java). The execution speed for the various types of tasks his software would need to do is extremely high with FORTRAN, although C was close behind and Java could be coaxed into running at almost half the speed, when geeky optimisations we won't won't go into here were performed on Linux. Apparently people have been burnt at the stake for much less. For the non-techies out there, FORTRAN is a very old language specially designed for writing scientific software. Programs written in it are extremely fast, but the language verges on a computer equivalent of Enochian, and is equally diabolical to write. The development time of the software will be much shorter with Java, so despite it not being an absolute asphalt-shredding speed-demon of a language, the first working version will be in Java, with a possibility of future translation into FORTRAN. Additionally, James has been itching to get back in to the lab, and to that extent he is preparing to go to town on the second form of hydroxyaluminosilicate, HAS-B, which is more complicated to study because it requires a lower concentration of aluminium, and appears to be more prone to dropping out of solution. Just to complicate matters further, HAS-A is actually a precursor to its formation! James plans to study particle sizes and zeta potentials, and again filter the solutions and examine the filtrate in the graphite furnace.

 

What’s On Page: Winter Update

Happy New Year and all that jazz. For one reason or another I haven’t updated this page in a while so this will be a big winter update. Anyway let’s start with the most important person, the right honourable Ian Stokes aka me.

Well for pretty much all of October I was away in sunny Athens, doing a little bit of work and a lot of riot dodging (I swear Chris is trying to kill me, I think he said my next research trip was on a boat off the coast of Somalia). When I wasn’t avoiding the revolution I was working with Panagiotis Apostolakos and Pantelis Livanos, learning a couple of methods for callose localisation. Some of Chris’s previous work has shown that callose may be involved in silica deposition, so knowing how to find it could be pretty useful.

Anyway the first method I looked at was staining with aniline blue, a simple method which can provide some pretty beautiful images, which I’m not going to explain because then I’d have to kill you afterwards.

 

The second method was secondary immunofluorescence, which is a little bit more complex. Without blinding you with science (or if I’m honest, blinding myself) it involves using two antibodies. The first primary antibody binds to the target (in this case callose). The second antibody carries the fluorophore (the bit that glows) and binds to the primary antibody. But enough with the techno-jargon, you came here to see cool glowing images, so here they are.

 

In amongst all the science I did manage to see a few sites though, so here’s a lovely picture of me being a tourist at the Temple of Poseidon.

 

Apart from being deployed into a foreign warzone, I’ve also been continuing my work on my Slovenia experiment. A few experiments here and there, most of which just proving that I didn’t mess up the original experiment but it all needs doing.

That’s all well and good but what about the less awesome people in the group you say? Well I suppose I could give them a quick mention. Matt has finally submitted his PhD thesis!!!!!! Then he went on a lovely trip to the bottom of a pint glass for a week or so and now he’s back and getting into the swing of his post-doc. The title of his Magnum opus is “Complementary studies of the role of metals in the conformation and interactions of serum amyloid P component and β-amyloid Aβ42”. He will now be preparing for his viva defence in February (I recommended an assault rifle but apparently that’s not going to cut it).

Matt, Emma and Chris also recently visited to Sweden to visit collaborators based in the student town of Lund and the slightly more energised and fast-paced city of Malmö. After a very productive three-day meeting (generating over 90 sides of A4 notes!!), they have decided upon a plan for the project and the next logical steps to be taken into the characterisation of aluminium-based-adjuvants, in vaccination preparations.

Last year, James went to Finland to visit some collaborators, with a view to reproducing some of the experiments and obtaining new results on more sensitive equipment. He also wanted to performing studies with different methods, for instance to find total surface charge. The results obtained in Finland have helped to shed light on the size and zeta-potential readings obtained at Keele. A combination of the Keele results and total surface charge measurements performed in Oulu has helped him to understand HASA particle formation a little better. James had also been using filtration combined with Graphite Furnace Atomic Absorption Spectroscopy to determine what proportion of Al (and therefore HAS particles) were actually "seen" by the equipment, and also to validate the particle size results obtained. The total surface charge measurements obtained in Oulu combined with the size and zeta-potential results obtained both at Keele and Oulu complement these data nicely. Whilst James was in Finland, we were horrified to hear that no one was likely to get any Christmas presents ever again as reindeer is a delicacy there and he reports that his main mission outside research was to find and eat Rudolph before he left.

More recently, James has been performing some simple computational simulations of the solutions that he was studying in Marvin (our particle sizer - a Malvern ZetaSizer) earlier in the year, which surprised him in the accuracy of their behaviour, especially as they were only initial investigations. They simulated several aspects of particle formation, including the buffering effect of aluminium hydroxide.

In December, he went to visit collaborators at the University of the Basque country in San Sebastian, northern Spain, in order to work on better and more comprehensive simulation designs, which he has begun coding. Finally, his 12-CPU (24 virtual CPU) behemoth will really be able to stretch its metaphorical legs on some real number-crunching! These new simulations should allow further detail to be simulated without excessive computational effort, and should also allow experimental results from both quantum simulations and benchtop chemistry, to be used directly as operating parameters. The model simulates collections of particles moving around in a box. It can optionally use the seminal "Metropolis" algorithm to govern particle motion (as the original 1953 paper did), but actually uses it primarily for governing "chemical reactions" between colliding particles. Much of the design work and some of the coding is done; however the remaining coding, some testing and some initial result taking are expected to dominate much of the start of this year. James never ceases to bore us with the fact that a derivative of computational methods used at the very dawn of computing in the 1940s and '50s, can still be relevant today and used on the latest hardware.

Last but not least, we have a new addition to the team. Krista Jones joined the team during September 2012 and is studying for a PhD. She will be researching the mechanisms involved in the production of hydroxyaluminosilicates (HAS) and the therapeutic potential of silicic acid in neurodegenerative disease. The purpose of this research is to discover the way in which aluminium binds to silicon to be excreted from the body, preventing and reducing aluminium accumulation in cells. Over the past few months she has been looking at silicon content in popular mineral waters using the Molybdenum Blue reaction and analysis by UV-VIS spectrophotometry. Over the coming months she hopse to achieve ethical approval for her patient study, investigating the therapeutic potential of silicic acid, as well as further analysis of samples by graphite furnace atomic absorption spectrophotometry GFAAS. Go check out her bio In the group members section for more information.